* Package:    sci-biology/pysam-0.17.0
 * Repository: gentoo
 * Maintainer: sci-biology@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox test userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/525c118216dd8499c08974e2fd9fd0f42279dd88  (Tue Apr  5 07:04:39 UTC 2022)
@@@@@ END @@@@@



##################
# emerge --info: #
##################
Portage 3.0.30 (python 3.10.4-final-0, default/linux/amd64/17.0/musl/hardened, gcc-11.2.1, musl-1.2.2-r8, 4.19.174-gentoo x86_64)
=================================================================
System uname: Linux-4.19.174-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-libc
KiB Mem:   264046488 total,  53985252 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Tue, 05 Apr 2022 07:04:38 +0000
sh bash 5.1_p16
ld GNU ld (Gentoo 2.38 p3) 2.38
app-misc/pax-utils:        1.3.3::gentoo
app-shells/bash:           5.1_p16::gentoo
dev-lang/perl:             5.34.1::gentoo
dev-lang/python:           3.8.13::gentoo, 3.9.12::gentoo, 3.10.4::gentoo
dev-util/cmake:            3.23.0::gentoo
dev-util/meson:            0.61.4-r2::gentoo
sys-apps/baselayout:       2.8::gentoo
sys-apps/openrc:           0.44.10::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-devel/autoconf:        2.71-r1::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.38-r1::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/gcc:             11.2.1_p20220115::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.7::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.17::gentoo (virtual/os-headers)
sys-libs/musl:             1.2.2-r8::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24
    sync-rsync-extra-opts: 

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* MIT"
CBUILD="x86_64-gentoo-linux-musl"
CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
CHOST="x86_64-gentoo-linux-musl"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
DISTDIR="/var/tmp/portage/sci-biology/pysam-0.17.0/distdir"
EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org"
INSTALL_MASK="charset.alias /usr/share/locale/locale.alias"
LANG="C.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j16"
PKGDIR="/root/tbci/binpkg"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
SHELL="/bin/bash"
USE="acl amd64 bzip2 crypt elogind hardened iconv ipv6 jumbo-build libglvnd libtirpc native-symlinks ncurses nls nptl openmp pam pcre pie readline seccomp split-usr ssl ssp test unicode xattr xtpax zlib" ABI_X86="64" ELIBC="musl" KERNEL="linux" PYTHON_TARGETS="python3_8 python3_9 python3_10" USERLAND="GNU"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS





##############################
# emerge history (qlop -mv): #
##############################
2022-04-05T08:29:09 >>> media-fonts/dejavu-2.37
2022-04-05T08:29:11 >>> sys-libs/timezone-data-2022a
2022-04-05T08:29:15 >>> sci-libs/htslib-1.13
2022-04-05T08:29:13 >>> media-fonts/stix-fonts-2.11
2022-04-05T08:29:20 >>> media-libs/libjpeg-turbo-2.1.3
2022-04-05T08:29:18 >>> media-libs/qhull-2020.2-r3
2022-04-05T08:29:24 >>> dev-python/six-1.16.0
2022-04-05T08:29:22 >>> dev-python/cython-0.29.28
2022-04-05T08:29:26 >>> dev-python/iniconfig-1.1.1
2022-04-05T08:29:28 >>> dev-python/pluggy-1.0.0-r1
2022-04-05T08:29:32 >>> dev-python/versioneer-0.22
2022-04-05T08:29:30 >>> dev-python/py-1.11.0-r1
2022-04-05T08:29:37 >>> dev-python/cppy-1.2.1-r1
2022-04-05T08:29:34 >>> dev-python/olefile-0.46-r1
2022-04-05T08:29:41 >>> dev-python/namespace-zope-1-r1
2022-04-05T08:29:43 >>> dev-python/setuptools_scm_git_archive-1.1-r4
2022-04-05T08:29:39 >>> dev-lang/nasm-2.15.05
2022-04-05T08:30:02 >>> dev-python/pytz-2022.1
2022-04-05T08:30:19 >>> dev-python/python-dateutil-2.8.2
2022-04-05T08:30:25 >>> dev-python/numpy-1.22.3
2022-04-05T08:30:42 >>> dev-python/kiwisolver-1.4.2
2022-04-05T08:30:47 >>> dev-python/cycler-0.11.0
2022-04-05T08:30:50 >>> dev-python/zope-interface-5.4.0
2022-04-05T08:30:55 >>> virtual/jpeg-100
2022-04-05T08:30:05 >>> sci-biology/samtools-1.13
2022-04-05T08:31:06 >>> dev-python/fs-2.4.15
2022-04-05T08:31:43 >>> dev-python/attrs-21.4.0
2022-04-05T08:31:46 >>> media-libs/tiff-4.3.0
2022-04-05T08:31:58 >>> dev-python/fonttools-4.31.2
2022-04-05T08:32:01 >>> dev-python/pytest-7.1.1
2022-04-05T08:32:04 >>> media-gfx/imagemagick-7.1.0.20-r1
2022-04-05T08:32:07 >>> dev-python/pillow-9.1.0
2022-04-05T08:32:27 >>> virtual/imagemagick-tools-0
2022-04-05T08:32:35 >>> dev-python/matplotlib-3.5.1
2022-04-05T08:32:49 >>> sci-biology/bcftools-1.13




#######################################
# installed packages (qlist -ICvUSS): #
#######################################
acct-group/audio-0-r1:0
acct-group/cdrom-0-r1:0
acct-group/dialout-0-r1:0
acct-group/disk-0-r1:0
acct-group/input-0-r1:0
acct-group/kmem-0-r1:0
acct-group/kvm-0-r1:0
acct-group/lp-0-r1:0
acct-group/man-0-r1:0
acct-group/messagebus-0-r1:0
acct-group/portage-0:0
acct-group/render-0-r1:0
acct-group/sgx-0:0
acct-group/sshd-0-r1:0
acct-group/tape-0-r1:0
acct-group/tty-0-r1:0
acct-group/video-0-r1:0
acct-user/man-1-r1:0
acct-user/messagebus-0-r1:0
acct-user/portage-0:0
acct-user/sshd-0-r1:0
app-admin/eselect-1.4.20:0 -doc -emacs -vim-syntax
app-admin/perl-cleaner-2.30:0
app-arch/bzip2-1.0.8-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static -static-libs
app-arch/gzip-1.11:0 -pic -static
app-arch/libarchive-3.6.0:0/13 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -blake2 bzip2 e2fsprogs -expat iconv -lz4 lzma -lzo -nettle -static-libs -verify-sig xattr -zstd
app-arch/tar-1.34:0 acl -minimal nls -selinux xattr
app-arch/unzip-6.0_p26:0 bzip2 -natspec unicode
app-arch/xz-utils-5.2.5-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 extra-filters nls split-usr -static-libs
app-arch/zstd-1.5.2:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -lz4 -static-libs threads
app-crypt/gnupg-2.3.4-r2:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -tpm -usb -user-socket -verify-sig -wks-server
app-crypt/gpgme-1.17.1:1/11.6.15 -common-lisp cxx -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -qt5 -static-libs -verify-sig
app-crypt/libb2-0.98.1-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -native-cflags openmp -static-libs
app-crypt/libmd-1.0.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
app-crypt/pinentry-1.2.0:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5
app-crypt/rhash-1.4.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls ssl -static-libs
app-editors/nano-6.2:0 -debug -justify -magic -minimal ncurses nls spell split-usr -static unicode
app-eselect/eselect-fontconfig-20220403:0
app-eselect/eselect-iptables-20220320:0
app-eselect/eselect-lib-bin-symlink-0.1.1-r1:0
app-eselect/eselect-pinentry-0.7.2:0
app-misc/c_rehash-1.7-r1:0
app-misc/ca-certificates-20211016.3.77:0 -cacert
app-misc/editor-wrapper-4-r1:0
app-misc/mime-types-2.1.53:0 -nginx
app-misc/pax-utils-1.3.3:0 -caps -debug -python -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 seccomp
app-misc/tmux-3.2a:0 -debug -selinux -utempter -vim-syntax
app-portage/eix-0.36.1:0 -debug -doc nls -sqlite
app-portage/elt-patches-20211104:0
app-portage/gemato-16.2:0 gpg -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -tools
app-portage/gentoolkit-0.5.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
app-portage/portage-utils-0.93.3:0 nls openmp qmanifest qtegrity -static
app-shells/bash-5.1_p16:0 -afs -bashlogger -examples -mem-scramble net nls -plugins readline
app-shells/push-3.4:0
app-shells/quoter-4.2:0
app-text/ansifilter-2.18:0 -qt5
app-text/build-docbook-catalog-2.2:0
app-text/docbook-xml-dtd-4.5-r2:4.5
app-text/docbook-xml-dtd-4.4-r3:4.4
app-text/docbook-xml-dtd-4.2-r3:4.2
app-text/docbook-xml-dtd-4.1.2-r7:4.1.2
app-text/docbook-xsl-stylesheets-1.79.1-r2:0 -ruby
app-text/manpager-1:0
app-text/sgml-common-0.6.3-r7:0
app-text/xmlto-0.0.28-r8:0 -latex -text
dev-db/sqlite-3.38.2:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -doc -icu readline -secure-delete -static-libs -tcl -test -tools
dev-lang/nasm-2.15.05:0 -doc
dev-lang/perl-5.34.1:0/5.34 -berkdb -debug -doc -gdbm ithreads -minimal -quadmath
dev-lang/python-3.10.4:3.10 -bluetooth -build -examples gdbm hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml
dev-lang/python-3.9.12:3.9 -bluetooth -build -examples gdbm hardened -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml
dev-lang/python-3.8.13:3.8 -bluetooth -build -examples gdbm hardened ncurses readline sqlite ssl -test -tk -verify-sig -wininst xml
dev-lang/python-exec-2.4.8:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-lang/python-exec-conf-2.4.6:2 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-lang/tcl-8.6.12:0/8.6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug threads
dev-libs/elfutils-0.186:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -lzma nls -static-libs -test -threads utils -valgrind -zstd
dev-libs/expat-2.4.8:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples -static-libs unicode
dev-libs/glib-2.72.0:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -dbus -debug elf -fam -gtk-doc mime -selinux -static-libs -sysprof -systemtap -test -utils xattr
dev-libs/gmp-6.2.1-r2:0/10.4 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cxx -doc -pic -static-libs
dev-libs/gobject-introspection-1.72.0:0 -doctool -gtk-doc -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -test
dev-libs/gobject-introspection-common-1.72.0:0
dev-libs/isl-0.24-r2:0/23 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
dev-libs/jsoncpp-1.9.5:0/25 -doc -test
dev-libs/libassuan-2.5.5:0
dev-libs/libbsd-0.11.6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -verify-sig
dev-libs/libevent-2.1.12:0/2.1-7 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 clock-gettime -debug -malloc-replacement ssl -static-libs -test threads -verbose-debug
dev-libs/libffi-3.4.2-r1:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -exec-static-trampoline -pax-kernel -static-libs -test
dev-libs/libgcrypt-1.10.1:0/20 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -cpu_flags_arm_aes -cpu_flags_arm_neon -cpu_flags_arm_sha1 -cpu_flags_arm_sha2 -cpu_flags_ppc_altivec -cpu_flags_ppc_vsx2 -cpu_flags_ppc_vsx3 cpu_flags_x86_aes cpu_flags_x86_avx cpu_flags_x86_avx2 -cpu_flags_x86_padlock -cpu_flags_x86_sha cpu_flags_x86_sse4_1 -doc o-flag-munging -static-libs -verify-sig
dev-libs/libgpg-error-1.44:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -common-lisp nls -static-libs
dev-libs/libksba-1.6.0:0 -static-libs
dev-libs/libltdl-2.4.7:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
dev-libs/libpcre-8.45-r1:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 cxx -jit -libedit pcre16 pcre32 readline split-usr -static-libs unicode zlib
dev-libs/libpcre2-10.39-r1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -jit -libedit pcre16 pcre32 readline split-usr -static-libs unicode zlib
dev-libs/libpipeline-1.5.5:0 -test
dev-libs/libtasn1-4.18.0:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -test -valgrind
dev-libs/libunistring-1.0:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -static-libs
dev-libs/libuv-1.44.1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
dev-libs/libxml2-2.9.13-r1:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -examples -icu -lzma python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 readline -static-libs -test
dev-libs/libxslt-1.1.35:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 crypt -debug -examples -static-libs
dev-libs/lzo-2.10:2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples split-usr -static-libs
dev-libs/mpc-1.2.1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
dev-libs/mpfr-4.1.0_p13-r1:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
dev-libs/nettle-3.7.3:0/8-6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm -cpu_flags_arm_neon cpu_flags_x86_aes -cpu_flags_x86_sha -doc gmp -static-libs -test
dev-libs/npth-1.6-r1:0
dev-libs/openssl-1.1.1n:0/1.1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cpu_flags_x86_sse2 -rfc3779 -sctp -sslv3 -static-libs -test -tls-compression -tls-heartbeat -vanilla -verify-sig -verify-sig
dev-libs/popt-1.18:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static-libs
dev-perl/Devel-CheckLib-1.140.0:0 -test
dev-perl/Encode-Locale-1.50.0-r1:0 -test
dev-perl/File-Listing-6.140.0:0 -test
dev-perl/HTML-Parser-3.760.0:0 -test
dev-perl/HTML-Tagset-3.200.0-r2:0
dev-perl/HTTP-Cookies-6.100.0:0 -test
dev-perl/HTTP-Date-6.50.0:0
dev-perl/HTTP-Message-6.330.0:0 -test -test
dev-perl/HTTP-Negotiate-6.10.0-r2:0 -test
dev-perl/IO-HTML-1.4.0:0 -test
dev-perl/IO-Socket-INET6-2.720.0-r2:0 -test
dev-perl/IO-Socket-SSL-2.74.0:0 -examples -idn -test
dev-perl/libwww-perl-6.600.0-r1:0 ssl -test
dev-perl/Locale-gettext-1.70.0-r1:0 -test
dev-perl/LWP-MediaTypes-6.40.0:0 -test
dev-perl/LWP-Protocol-https-6.100.0:0 -test
dev-perl/Module-Build-0.423.100:0 -test
dev-perl/Mozilla-CA-20999999-r1:0 -test
dev-perl/Net-HTTP-6.210.0:0 -minimal -test
dev-perl/Net-SSLeay-1.900.0:0 -examples -examples -minimal -test
dev-perl/Socket6-0.290.0:0 -test
dev-perl/TimeDate-2.330.0-r1:0 -test
dev-perl/Try-Tiny-0.310.0:0 -minimal -test
dev-perl/URI-5.100.0:0 -test
dev-perl/WWW-RobotRules-6.20.0-r2:0 -test
dev-perl/XML-Parser-2.460.0-r2:0
dev-python/appdirs-1.4.4-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/attrs-21.4.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/certifi-3021.3.16-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/charset_normalizer-2.0.12:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/cppy-1.2.1-r1:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/cycler-0.11.0:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
dev-python/cython-0.29.28:0 -doc -emacs -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/flit_core-3.7.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/fonttools-4.31.2:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -test
dev-python/fs-2.4.15:0 -doc python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/idna-3.3:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/importlib_metadata-4.11.3:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/importlib_resources-5.6.0:0 -doc -python_targets_pypy3 python_targets_python3_8 -test
dev-python/iniconfig-1.1.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/installer-0.5.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jaraco-context-4.1.1-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jaraco-functools-3.5.0-r2:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jaraco-text-3.7.0-r2:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jinja-3.1.1:0 -doc -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/kiwisolver-1.4.2:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/markupsafe-2.1.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/matplotlib-3.5.1:0 -cairo -doc -examples -excel -gtk3 -latex python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -qt5 -test -test -tk -webagg -wxwidgets
dev-python/more-itertools-8.12.0-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/namespace-zope-1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/nspektr-0.3.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/numpy-1.22.3:0 -doc -lapack python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/olefile-0.46-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/ordered-set-4.1.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/packaging-21.3-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pillow-9.1.0:0 -examples -imagequant jpeg -jpeg2k -lcms -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test -test tiff -tk truetype -webp -xcb zlib
dev-python/pluggy-1.0.0-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/py-1.11.0-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pyparsing-3.0.7-r1:0 -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pypax-0.9.5-r1:0 -ptpax python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 xtpax
dev-python/PySocks-1.7.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/pytest-7.1.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/python-dateutil-2.8.2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pytz-2022.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-python/requests-2.27.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -socks5 -test
dev-python/setuptools-61.3.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/setuptools_scm-6.4.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/setuptools_scm_git_archive-1.1-r4:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/six-1.16.0:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/tomli-2.0.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/urllib3-1.26.9:0 -brotli -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/versioneer-0.22:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 test
dev-python/wheel-0.37.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/zipp-3.8.0:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/zope-interface-5.4.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-util/cmake-3.23.0:0 -doc -emacs ncurses -qt5 -test -test
dev-util/desktop-file-utils-0.26-r2:0 -emacs
dev-util/glib-utils-2.72.0:0 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9
dev-util/gperf-3.1:0
dev-util/gtk-doc-am-1.33.2:0
dev-util/intltool-0.51.0-r2:0
dev-util/meson-0.61.4-r2:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-util/meson-format-array-0:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9
dev-util/ninja-1.10.2-r1:0 -doc -emacs -test -vim-syntax
dev-util/pkgconf-1.8.0-r1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -test
dev-util/re2c-2.2:0 -debug -test
dev-vcs/git-2.35.1:0 blksha1 -cgi curl -cvs -doc -emacs -gnome-keyring gpg -highlight iconv -mediawiki -mediawiki-experimental nls pcre -perforce -perl -ppcsha1 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9 -subversion -test threads -tk webdav -xinetd
media-fonts/dejavu-2.37:0 -X -fontforge
media-fonts/liberation-fonts-2.1.3:0 -X -X -fontforge
media-fonts/stix-fonts-2.11:0 -X
media-gfx/graphite2-1.3.14_p20210810-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -perl -test
media-gfx/imagemagick-7.1.0.20-r1:0/7.1.0-0 -X bzip2 -corefonts cxx -djvu -fftw -fontconfig -fpx -graphviz -hdri -heif -jbig jpeg -jpeg2k -lcms -lqr -lzma -opencl -openexr openmp -pango -perl png -postscript -q32 -q8 -raw -static-libs -svg -test tiff -truetype -webp -wmf -xml -zip zlib
media-libs/fontconfig-2.14.0-r1:1.0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -static-libs -test
media-libs/freetype-2.12.0:2 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 adobe-cff -brotli bzip2 cleartype-hinting -debug -doc -fontforge harfbuzz -infinality png -static-libs -svg -utils
media-libs/harfbuzz-4.2.0:0/4.0.0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cairo -debug -doc -experimental glib graphite -icu introspection -test truetype
media-libs/libjpeg-turbo-2.1.3:0/0.2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_neon -java -java -static-libs
media-libs/libpng-1.6.37-r2:0/16 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -apng -cpu_flags_arm_neon cpu_flags_x86_sse -static-libs
media-libs/qhull-2020.2-r3:0/8 -doc -static-libs
media-libs/tiff-4.3.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cxx -jbig jpeg -lzma -static-libs -test -webp zlib -zstd
net-dns/libidn2-2.3.2:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -verify-sig
net-firewall/iptables-1.8.7-r2:0/1.8.3 -conntrack -netlink -nftables -pcap split-usr -static-libs
net-libs/gnutls-3.7.3-r1:0/30 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cxx -dane -doc -examples -guile idn nls openssl -pkcs11 seccomp -sslv2 -sslv3 -static-libs -test -test-full tls-heartbeat -tools -valgrind
net-libs/libmnl-1.0.4:0/0.2.0 -examples split-usr -static-libs -verify-sig
net-libs/nghttp2-1.47.0:0/1.14 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cxx -debug -hpack-tools -jemalloc -static-libs -test threads -utils -xml
net-misc/curl-7.82.0-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -adns -alt-svc -brotli -curl_ssl_gnutls -curl_ssl_mbedtls -curl_ssl_nss curl_ssl_openssl ftp -gnutls -gopher -hsts http2 -idn imap ipv6 -kerberos -ldap -mbedtls -nghttp3 -nss openssl pop3 progress-meter -quiche -rtmp -samba smtp -ssh ssl -sslv3 -static-libs -telnet -test tftp -threads -zstd
net-misc/iputils-20211215:0 arping -caps -clockdiff -doc filecaps -gcrypt -idn -nettle nls -rarpd -rdisc ssl -static -test -tracepath
net-misc/netifrc-0.7.3:0
net-misc/openssh-8.9_p1-r2:0 -X -X509 -abi_mips_n32 -audit -debug -hpn -kerberos -ldns -libedit -livecd pam pie scp -sctp -security-key -selinux ssl -static -test -verify-sig -xmss
net-misc/rsync-3.2.3-r5:0 acl -examples iconv ipv6 -lz4 ssl -stunnel -system-zlib -verify-sig xattr -xxhash -zstd
net-misc/wget-1.21.3:0 -cookie-check -debug -gnutls -idn ipv6 -metalink nls -ntlm pcre ssl -static -test -uuid zlib
perl-core/CPAN-2.290.0-r1:0
perl-core/Encode-3.120.0:0
perl-core/File-Temp-0.231.100:0
perl-core/Scalar-List-Utils-1.560.0:0
sci-biology/bcftools-1.13:0 -python_single_target_python3_10 -python_single_target_python3_8 python_single_target_python3_9
sci-biology/samtools-1.13:0
sci-libs/htslib-1.13:0/3 bzip2 -curl lzma
sec-keys/openpgp-keys-gentoo-release-20220101:0 -test
sys-apps/acl-2.3.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls split-usr -static-libs
sys-apps/attr-2.5.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls split-usr -static-libs
sys-apps/baselayout-2.8:0 -build split-usr
sys-apps/coreutils-9.0-r2:0 acl -caps -gmp -hostname -kill -multicall nls -selinux split-usr -static -test -vanilla xattr
sys-apps/dbus-1.14.0:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -doc elogind -selinux -static-libs -systemd -test -test
sys-apps/debianutils-5.7:0 installkernel -static
sys-apps/diffutils-3.8:0 nls -static
sys-apps/elfix-0.9.5:0 -ptpax xtpax
sys-apps/file-5.41:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -lzma -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -seccomp -static-libs zlib
sys-apps/findutils-4.9.0:0 nls -selinux -static -test
sys-apps/gawk-5.1.1-r1:0 -mpfr nls readline
sys-apps/gentoo-functions-0.15:0
sys-apps/grep-3.7:0 nls pcre -static
sys-apps/groff-1.22.4:0 -X -examples -uchardet
sys-apps/help2man-1.48.5:0 nls
sys-apps/install-xattr-0.8:0
sys-apps/iproute2-5.17.0:0 -atm -berkdb -bpf -caps -elf iptables -libbsd -minimal -selinux
sys-apps/kbd-2.4.0:0 nls pam -test
sys-apps/kmod-29:0 -debug -doc lzma -pkcs7 -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -static-libs tools zlib -zstd
sys-apps/less-590:0 pcre unicode
sys-apps/man-db-2.10.2:0 -berkdb manpager -nls seccomp -selinux -static-libs zlib
sys-apps/net-tools-2.10:0 arp hostname ipv6 -nis nls -plipconfig -selinux -slattach -static
sys-apps/openrc-0.44.10:0 -audit -bash -debug ncurses netifrc -newnet pam -selinux -sysv-utils unicode
sys-apps/portage-3.0.30-r1:0 -apidoc -build -doc -gentoo-dev ipc native-extensions -python_targets_pypy3 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 rsync-verify -selinux -test xattr
sys-apps/sandbox-2.29:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nnp
sys-apps/sed-4.8:0 acl nls -selinux -static
sys-apps/shadow-4.11.1:0/4 acl -audit -bcrypt -cracklib nls pam -selinux -skey split-usr -su xattr
sys-apps/systemd-tmpfiles-249.9:0 -selinux -test
sys-apps/sysvinit-3.01:0 -ibm -selinux -static
sys-apps/texinfo-6.8:0 nls standalone -static
sys-apps/util-linux-2.38:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -build -caps cramfs -cryptsetup -fdformat hardlink -kill logger -magic ncurses nls pam -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 readline -rtas -selinux -slang split-usr -static-libs su suid -systemd -test -tty-helpers -udev unicode -verify-sig
sys-apps/which-2.21:0
sys-auth/elogind-246.10-r2:0 acl -audit cgroup-hybrid -debug -doc pam -policykit -selinux
sys-auth/pambase-20220214:0 -caps -debug elogind -gnome-keyring -homed -minimal -mktemp nullok -pam_krb5 -pam_ssh passwdqc -pwhistory -pwquality -securetty -selinux sha512 -systemd -yescrypt
sys-auth/passwdqc-2.0.2-r1:0
sys-devel/autoconf-2.71-r1:2.71 -emacs
sys-devel/autoconf-archive-2022.02.11:0
sys-devel/autoconf-wrapper-20220130:0
sys-devel/automake-1.16.5:1.16 -test
sys-devel/automake-wrapper-11:0
sys-devel/binutils-2.38-r1:2.38 -cet -default-gold -doc gold -multitarget nls -pgo plugins -static-libs -test -vanilla
sys-devel/binutils-config-5.4.1:0 native-symlinks
sys-devel/bison-3.8.2:0 -examples nls -static -test
sys-devel/flex-2.6.4-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static -test
sys-devel/gcc-11.2.1_p20220115:11 -ada -cet -custom-cflags cxx -d -debug -doc -fixed-point -fortran -go graphite hardened -jit -libssp lto -multilib -nls nptl -objc -objc++ -objc-gc openmp -pch -pgo pie -sanitize ssp -systemtap -test -valgrind -vanilla -vtv -zstd
sys-devel/gcc-config-2.5-r1:0 cc-wrappers native-symlinks
sys-devel/gettext-0.21-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -cvs cxx -doc -emacs -git -java -java ncurses -nls openmp -static-libs
sys-devel/gnuconfig-20210107:0
sys-devel/libtool-2.4.7:2 -vanilla
sys-devel/m4-1.4.19:0 -examples nls
sys-devel/make-4.3:0 -guile nls -static
sys-devel/patch-2.7.6-r4:0 -static -test xattr
sys-fs/e2fsprogs-1.46.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cron -fuse -lto -nls split-usr -static-libs threads tools
sys-fs/udev-249.9:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl kmod -selinux split-usr -test
sys-fs/udev-init-scripts-35:0
sys-kernel/installkernel-gentoo-5:0 -grub
sys-kernel/linux-headers-5.17:0 -headers-only
sys-libs/argp-standalone-1.4.1-r1:0 -static-libs
sys-libs/binutils-libs-2.38-r1:0/2.38 -64-bit-bfd -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cet -multitarget nls -static-libs
sys-libs/fts-standalone-1.2.7:0 -static-libs
sys-libs/gdbm-1.23:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 berkdb nls readline -static-libs
sys-libs/libcap-2.63:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 pam split-usr -static-libs -tools
sys-libs/libseccomp-2.5.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -python python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -static-libs -test
sys-libs/musl-1.2.2-r8:0 -headers-only
sys-libs/ncurses-6.3_p20211106:0/6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -ada cxx -debug -doc -gpm -minimal -profile split-usr -static-libs -test tinfo -trace
sys-libs/obstack-standalone-1.1:0 -static-libs
sys-libs/pam-1.5.2-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -audit -berkdb -debug -filecaps -nis -selinux
sys-libs/readline-8.1_p2:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static-libs unicode -utils
sys-libs/timezone-data-2022a:0 -leaps-timezone nls -zic-slim
sys-libs/zlib-1.2.12-r2:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 minizip split-usr -static-libs -verify-sig
sys-process/procps-3.3.17-r1:0/8 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 elogind kill -modern-top ncurses nls -selinux split-usr -static-libs -systemd -test unicode
sys-process/psmisc-23.4-r1:0 -X ipv6 nls -selinux
virtual/acl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
virtual/awk-1:0
virtual/dev-manager-0-r2:0
virtual/editor-0-r3:0
virtual/imagemagick-tools-0:0 jpeg -perl -png -svg tiff
virtual/jpeg-100:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
virtual/libc-1-r1:0
virtual/libcrypt-1-r1:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs
virtual/libelf-3:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
virtual/libiconv-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
virtual/libintl-0-r2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
virtual/libudev-232-r5:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -systemd
virtual/man-0-r4:0
virtual/os-headers-0-r2:0
virtual/package-manager-1:0
virtual/pager-0:0
virtual/perl-Carp-1.520.0-r1:0
virtual/perl-Compress-Raw-Bzip2-2.101.0:0
virtual/perl-Compress-Raw-Zlib-2.101.0:0
virtual/perl-CPAN-2.290.0:0
virtual/perl-CPAN-Meta-2.150.10-r5:0
virtual/perl-CPAN-Meta-Requirements-2.140.0-r7:0
virtual/perl-CPAN-Meta-YAML-0.18.0-r7:0
virtual/perl-Data-Dumper-2.179.0:0
virtual/perl-Digest-MD5-2.580.0:0
virtual/perl-Encode-3.120.0:0
virtual/perl-Exporter-5.760.0:0
virtual/perl-ExtUtils-CBuilder-0.280.236:0
virtual/perl-ExtUtils-Install-2.200.0:0
virtual/perl-ExtUtils-MakeMaker-7.620.0:0
virtual/perl-ExtUtils-Manifest-1.730.0:0
virtual/perl-ExtUtils-ParseXS-3.430.0:0
virtual/perl-File-Spec-3.800.0:0
virtual/perl-File-Temp-0.231.100:0
virtual/perl-Getopt-Long-2.520.0:0
virtual/perl-IO-1.460.0:0
virtual/perl-IO-Compress-2.102.0:0
virtual/perl-IO-Socket-IP-0.410.0:0
virtual/perl-JSON-PP-4.60.0:0
virtual/perl-libnet-3.130.0:0 ssl
virtual/perl-MIME-Base64-3.160.0:0
virtual/perl-Module-Metadata-1.0.37-r1:0
virtual/perl-parent-0.238.0-r1:0
virtual/perl-Parse-CPAN-Meta-2.150.10-r5:0
virtual/perl-Perl-OSType-1.10.0-r5:0
virtual/perl-podlators-4.140.0-r2:0
virtual/perl-Scalar-List-Utils-1.560.0:0
virtual/perl-Test-Harness-3.430.0:0
virtual/perl-Text-ParseWords-3.300.0-r8:0
virtual/perl-Time-Local-1.300.0:0
virtual/perl-version-0.992.800:0
virtual/perl-XSLoader-0.300.0-r4:0
virtual/pkgconfig-2-r1:0
virtual/service-manager-1:0
virtual/ssh-0:0 -minimal
virtual/tmpfiles-0-r1:0
virtual/ttf-fonts-1-r1:0
virtual/udev-217-r3:0
virtual/yacc-0:0
www-client/pybugz-0.13-r1:0 python_targets_python3_8 python_targets_python3_9
x11-libs/cairo-1.16.0-r5:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only glib -opengl -static-libs svg -utils -valgrind
x11-libs/pixman-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 cpu_flags_x86_ssse3 -loongson2f -static-libs
x11-misc/shared-mime-info-2.2:0 -test


#######################
# build.log           #
#######################
>>> Unpacking source...
>>> Unpacking pysam-0.17.0.tar.gz to /var/tmp/portage/sci-biology/pysam-0.17.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/pysam-0.17.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0 ...
 * Building test data
make -j16 -C tests/pysam_data 
make: Entering directory '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0/tests/pysam_data'
samtools faidx ex1.fa
gunzip < ex1.sam.gz > ex1.sam
samtools view --no-PG -bo ex10.bam ex10.sam
samtools view --no-PG -bo ex3.bam ex3.sam
samtools view --no-PG -bo ex4.bam ex4.sam
samtools view --no-PG -bo ex5.bam ex5.sam
samtools view --no-PG -bo ex6.bam ex6.sam
samtools view --no-PG -bo ex8.bam ex8.sam
samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam
samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam
samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam
samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam
samtools view --no-PG -bo example_btag.bam example_btag.sam
samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam
samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam
samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam
samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam
touch tmp.list
samtools view --no-PG -bo issue100.bam issue100.sam
samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam
samtools view --no-PG -bo softclip.bam softclip.sam
samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam
samtools view --no-PG -bo tag_bug.bam tag_bug.sam
samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam
samtools view --no-PG -bo test_query_position.bam test_query_position.sam
samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam
samtools index ex10.bam
samtools index ex3.bam
rm -f tmp.list
samtools index ex4.bam
samtools index ex5.bam
samtools index ex6.bam
samtools index ex8.bam
samtools index ex9_fail.bam
samtools index ex9_nofail.bam
samtools index ex_spliced.bam
samtools index example_aligned_pairs.bam
samtools index example_btag.bam
samtools index example_dash_in_chr.bam
samtools index example_empty_header.bam
samtools index example_empty_with_header.bam
samtools index example_reverse_complement.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index issue100.bam
samtools index softclip.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index test_query_position.bam
samtools index test_unaligned.bam
samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam
samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz
samtools faidx ex1.fa.gz
samtools index ex3.cram
samtools index rg_with_tab.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
samtools index ex1.bam
cp ex1.bam example_bai.bam
cp ex1.bam explicit_index.bam
cp ex1.bam ex1_csi.bam
samtools index example_bai.bam
samtools index -c ex1_csi.bam
[mpileup] 1 samples in 1 input files
samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz
mv example_bai.bam.bai example_bai.bai
samtools index ex1.cram
cp ex1.cram explicit_index.cram
gunzip < ex2.sam.gz > ex2.sam
samtools view --no-PG -bo ex2.bam ex2.sam
samtools view --no-PG -bu -o uncompressed.bam ex2.sam
samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam
grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam -
samtools index empty.bam
samtools index ex2.bam
samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
head -c 124000 ex2.bam > ex2_truncated.bam
(bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
samtools index ex2.cram
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view --no-PG -bo with_md.bam with_md.sam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
touch all.stamp
rm with_md.sam
make: Leaving directory '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0/tests/pysam_data'
make -j16 -C tests/cbcf_data 
make: Entering directory '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0/tests/cbcf_data'
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
bgzip < example_vcf43.vcf > example_vcf43.vcf.gz
tabix -p vcf example_vcf40.vcf.gz    # create tbi index
bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf example_vcf42.vcf.gz    # create tbi index
tabix -p vcf example_vcf42_only_header.vcf.gz    # create tbi index
bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz    # create tbi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf example_vcf43.vcf.gz    # create tbi index
bcftools index example_vcf40.vcf.gz  # create csi index
tabix -p vcf example_vcf43_with_utf8.vcf.gz    # create tbi index
bcftools index example_vcf42_only_header.vcf.gz  # create csi index
tabix -p vcf gnomad.vcf.gz    # create tbi index
bcftools index example_vcf42.vcf.gz  # create csi index
tabix -p vcf missing_genotypes.vcf.gz    # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz  # create csi index
tabix -p vcf gnomad_fixed.vcf.gz    # create tbi index
bcftools index example_vcf43.vcf.gz  # create csi index
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf43_with_utf8.vcf.gz  # create csi index
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf40.bcf
bcftools index missing_genotypes.vcf.gz  # create csi index
bcftools index gnomad_fixed.vcf.gz  # create csi index
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf
bcftools index gnomad.vcf.gz  # create csi index
bcftools index example_vcf42_only_header.bcf
bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf43.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index example_vcf43_with_utf8.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
bcftools index missing_genotypes.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=Gbcftools view -O b gnomad.vcf.gz -o gnomad.bcf

bcftools index gnomad_fixed.bcf
bcftools index gnomad.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
touch all.stamp
make: Leaving directory '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0/tests/cbcf_data'
 * Will copy sources from /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0
 * python3_8: copying to /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8
 * python3_9: copying to /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9
 * python3_10: copying to /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0 ...
 * python3_8: running distutils-r1_run_phase python_compile
python3.8 setup.py build_ext --inplace -j1
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
cythoning pysam/libcutils.pyx to pysam/libcutils.c
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
cythoning pysam/libctabix.pyx to pysam/libctabix.c
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
building 'pysam.libchtslib' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libchtslib.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/htslib_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libchtslib.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/lz4
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_ampliconclip.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/amplicon_stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/tmp_file.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_ampliconclip.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/amplicon_stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/lz4/lz4.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcsamtools.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/str_finder.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/extsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/dist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/abuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcftools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/str_finder.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/extsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/dist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/abuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/HMM.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcbcftools.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcsamtools.cpython-38-x86_64-linux-gnu -lcbcftools.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcutils.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:28437:16: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
28437 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:14154:20: warning: ignoring return value of 'sam_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
14154 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcalignmentfile.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcsamfile.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
pysam/libcalignedsegment.c:14555:10: warning: ignoring return value of 'sam_parse1' declared with attribute 'warn_unused_result' [-Wunused-result]
14555 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcalignedsegment.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libctabix.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcfaidx.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_6close':
pysam/libcbcf.c:66841:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66841 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__':
pysam/libcbcf.c:66566:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66566 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_f_5pysam_7libcbcf_11VariantFile_write':
pysam/libcbcf.c:71684:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
71684 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample':
pysam/libcbcf.c:35650:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35650 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta':
pysam/libcbcf.c:35350:11: warning: ignoring return value of 'bcf_hrec_add_key' declared with attribute 'warn_unused_result' [-Wunused-result]
35350 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35376:11: warning: ignoring return value of 'bcf_hrec_set_val' declared with attribute 'warn_unused_result' [-Wunused-result]
35376 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35489:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35489 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line':
pysam/libcbcf.c:34915:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34915 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record':
pysam/libcbcf.c:34780:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34780 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcbcf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcbgzf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libctabixproxies.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcvcf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libchtslib.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcsamtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcbcftools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcutils.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2564:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2569:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2613:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2618:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcsamfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcalignedsegment.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libctabix.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcfaidx.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcbcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcbgzf.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libctabixproxies.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam/libcvcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
python3.8 setup.py build -j 16 -j1
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/config.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/version.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/utils.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/samtools.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/bcftools.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/Pileup.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include
copying pysam/include/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcvcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcutils.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libctabixproxies.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libctabix.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcsamtools.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcsamfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libchtslib.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcfaidx.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcbcftools.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcbcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcalignmentfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/libcalignedsegment.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/version.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/pysam_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/pysam_stream.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/htslib_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/csamtools_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
copying pysam/cbcftools_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/samtools_config_vars.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/config.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/tmp_file.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/stats_isize.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/samtools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/samtools.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/sample.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/sam_opts.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/sam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bedidx.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bam_plbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bam_lpileup.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bam_endian.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
copying samtools/bam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/samtools
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/config.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/vcmp.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/variantkey.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/utlist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/str_finder.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/rbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/prob1.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/ploidy.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/mw.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/kmin.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/kheap.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/hex.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/hclust.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/gvcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/filter.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/extsort.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/dist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/convert.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/cols.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/call.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/bin.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/bcftools.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/bam_sample.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/abuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
copying bcftools/HMM.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/include/bcftools
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libchtslib.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/htslib_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libchtslib.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_ampliconclip.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/amplicon_stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/tmp_file.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_ampliconclip.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/amplicon_stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/samtools/lz4/lz4.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcsamtools.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/str_finder.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/extsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/dist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/abuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcftools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/str_finder.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/extsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/dist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/abuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/bcftools/HMM.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcbcftools.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcsamtools.cpython-38-x86_64-linux-gnu -lcbcftools.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcutils.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:28437:16: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
28437 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:14154:20: warning: ignoring return value of 'sam_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
14154 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcalignmentfile.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcsamfile.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
pysam/libcalignedsegment.c:14555:10: warning: ignoring return value of 'sam_parse1' declared with attribute 'warn_unused_result' [-Wunused-result]
14555 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcalignedsegment.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libctabix.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcfaidx.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_6close':
pysam/libcbcf.c:66841:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66841 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__':
pysam/libcbcf.c:66566:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66566 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_f_5pysam_7libcbcf_11VariantFile_write':
pysam/libcbcf.c:71684:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
71684 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample':
pysam/libcbcf.c:35650:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35650 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta':
pysam/libcbcf.c:35350:11: warning: ignoring return value of 'bcf_hrec_add_key' declared with attribute 'warn_unused_result' [-Wunused-result]
35350 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35376:11: warning: ignoring return value of 'bcf_hrec_set_val' declared with attribute 'warn_unused_result' [-Wunused-result]
35376 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35489:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35489 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line':
pysam/libcbcf.c:34915:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34915 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record':
pysam/libcbcf.c:34780:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34780 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcbcf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcbgzf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libctabixproxies.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8 -I/usr/include/python3.8 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/temp.linux-x86_64-3.8/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-38-x86_64-linux-gnu -lcutils.cpython-38-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/build/lib/pysam/libcvcf.cpython-38-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
 * python3_9: running distutils-r1_run_phase python_compile
python3.9 setup.py build_ext --inplace -j1
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libchtslib.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcsamtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcbcftools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcutils.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2564:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2569:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2613:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2618:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcsamfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcalignedsegment.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libctabix.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcfaidx.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcbcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcbgzf.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libctabixproxies.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcvcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libchtslib.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/amplicon_stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_ampliconclip.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/abuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/dist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/extsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/str_finder.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/abuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/dist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/extsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/str_finder.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcsamtools.cpython-39-x86_64-linux-gnu -lcbcftools.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:28437:16: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
28437 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:14154:20: warning: ignoring return value of 'sam_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
14154 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
pysam/libcalignedsegment.c:14555:10: warning: ignoring return value of 'sam_parse1' declared with attribute 'warn_unused_result' [-Wunused-result]
14555 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_6close':
pysam/libcbcf.c:66841:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66841 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__':
pysam/libcbcf.c:66566:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66566 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_f_5pysam_7libcbcf_11VariantFile_write':
pysam/libcbcf.c:71684:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
71684 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample':
pysam/libcbcf.c:35650:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35650 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta':
pysam/libcbcf.c:35350:11: warning: ignoring return value of 'bcf_hrec_add_key' declared with attribute 'warn_unused_result' [-Wunused-result]
35350 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35376:11: warning: ignoring return value of 'bcf_hrec_set_val' declared with attribute 'warn_unused_result' [-Wunused-result]
35376 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35489:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35489 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line':
pysam/libcbcf.c:34915:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34915 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record':
pysam/libcbcf.c:34780:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34780 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
python3.9 setup.py build -j 16 -j1
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/config.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/version.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/utils.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/samtools.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/bcftools.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/Pileup.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include
copying pysam/include/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcvcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcutils.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libctabixproxies.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libctabix.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcsamtools.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcsamfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libchtslib.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcfaidx.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcbcftools.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcbcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcalignmentfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/libcalignedsegment.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/version.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/pysam_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/pysam_stream.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/htslib_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/csamtools_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
copying pysam/cbcftools_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/samtools_config_vars.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/config.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/tmp_file.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/stats_isize.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/samtools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/samtools.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/sample.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/sam_opts.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/sam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bedidx.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_plbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_lpileup.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_endian.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
copying samtools/bam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/samtools
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/config.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/vcmp.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/variantkey.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/utlist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/str_finder.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/rbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/prob1.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/ploidy.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/mw.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/kmin.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/kheap.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/hex.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/hclust.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/gvcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/filter.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/extsort.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/dist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/convert.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/cols.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/call.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bin.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bcftools.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bam_sample.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/abuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
copying bcftools/HMM.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/include/bcftools
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libchtslib.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/amplicon_stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_ampliconclip.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/abuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/dist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/extsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/str_finder.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/abuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/dist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/extsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/str_finder.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcsamtools.cpython-39-x86_64-linux-gnu -lcbcftools.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:28437:16: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
28437 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:14154:20: warning: ignoring return value of 'sam_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
14154 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
pysam/libcalignedsegment.c:14555:10: warning: ignoring return value of 'sam_parse1' declared with attribute 'warn_unused_result' [-Wunused-result]
14555 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_6close':
pysam/libcbcf.c:66841:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66841 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__':
pysam/libcbcf.c:66566:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66566 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_f_5pysam_7libcbcf_11VariantFile_write':
pysam/libcbcf.c:71684:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
71684 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample':
pysam/libcbcf.c:35650:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35650 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta':
pysam/libcbcf.c:35350:11: warning: ignoring return value of 'bcf_hrec_add_key' declared with attribute 'warn_unused_result' [-Wunused-result]
35350 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35376:11: warning: ignoring return value of 'bcf_hrec_set_val' declared with attribute 'warn_unused_result' [-Wunused-result]
35376 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35489:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35489 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line':
pysam/libcbcf.c:34915:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34915 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record':
pysam/libcbcf.c:34780:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34780 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9 -I/usr/include/python3.9 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/temp.linux-x86_64-3.9/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_9/build/lib/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
 * python3_10: running distutils-r1_run_phase python_compile
python3.10 setup.py build_ext --inplace -j1
/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils import log
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libchtslib.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcsamtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcbcftools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcutils.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2564:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2569:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2613:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2618:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcsamfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcalignedsegment.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libctabix.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcfaidx.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcbcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcbgzf.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libctabixproxies.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python3.10/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcvcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libchtslib.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/lz4
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/amplicon_stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_ampliconclip.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/abuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/dist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/extsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/str_finder.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcsamtools.cpython-310-x86_64-linux-gnu -lcbcftools.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcutils.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:28437:16: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
28437 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:14154:20: warning: ignoring return value of 'sam_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
14154 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
pysam/libcalignedsegment.c:14555:10: warning: ignoring return value of 'sam_parse1' declared with attribute 'warn_unused_result' [-Wunused-result]
14555 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libctabix.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_6close':
pysam/libcbcf.c:66841:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66841 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__':
pysam/libcbcf.c:66566:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66566 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_f_5pysam_7libcbcf_11VariantFile_write':
pysam/libcbcf.c:71684:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
71684 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample':
pysam/libcbcf.c:35650:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35650 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta':
pysam/libcbcf.c:35350:11: warning: ignoring return value of 'bcf_hrec_add_key' declared with attribute 'warn_unused_result' [-Wunused-result]
35350 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35376:11: warning: ignoring return value of 'bcf_hrec_set_val' declared with attribute 'warn_unused_result' [-Wunused-result]
35376 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35489:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35489 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line':
pysam/libcbcf.c:34915:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34915 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record':
pysam/libcbcf.c:34780:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34780 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
python3.10 setup.py build -j 16 -j1
/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
  from distutils import log
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/config.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/version.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/utils.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/samtools.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/bcftools.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/Pileup.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include
copying pysam/include/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcvcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcutils.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libctabixproxies.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libctabix.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcsamtools.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcsamfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libchtslib.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcfaidx.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcbcftools.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcbcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcalignmentfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/libcalignedsegment.pxd -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/version.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/pysam_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/pysam_stream.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/htslib_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/csamtools_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
copying pysam/cbcftools_util.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/samtools_config_vars.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/config.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/tmp_file.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/stats_isize.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/samtools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/samtools.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/sample.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/sam_opts.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/sam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bedidx.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bam_plbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bam_lpileup.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bam_endian.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
copying samtools/bam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/samtools
creating /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/config.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/vcmp.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/variantkey.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/utlist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/str_finder.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/rbuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/prob1.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/ploidy.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/mw.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/kmin.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/kheap.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/hex.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/hclust.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/gvcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/filter.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/extsort.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/dist.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/convert.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/cols.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/call.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/bin.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/bcftools.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/bam_sample.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/abuf.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
copying bcftools/HMM.h -> /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/include/bcftools
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libchtslib.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/amplicon_stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_ampliconclip.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/abuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/dist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/extsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/str_finder.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcsamtools.cpython-310-x86_64-linux-gnu -lcbcftools.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcutils.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
pysam/libcalignmentfile.c:28437:16: warning: ignoring return value of 'bgzf_seek' declared with attribute 'warn_unused_result' [-Wunused-result]
28437 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
pysam/libcalignmentfile.c:14154:20: warning: ignoring return value of 'sam_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
14154 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
pysam/libcalignedsegment.c:14555:10: warning: ignoring return value of 'sam_parse1' declared with attribute 'warn_unused_result' [-Wunused-result]
14555 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libctabix.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_6close':
pysam/libcbcf.c:66841:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66841 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__':
pysam/libcbcf.c:66566:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
66566 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_f_5pysam_7libcbcf_11VariantFile_write':
pysam/libcbcf.c:71684:18: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result]
71684 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample':
pysam/libcbcf.c:35650:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35650 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta':
pysam/libcbcf.c:35350:11: warning: ignoring return value of 'bcf_hrec_add_key' declared with attribute 'warn_unused_result' [-Wunused-result]
35350 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35376:11: warning: ignoring return value of 'bcf_hrec_set_val' declared with attribute 'warn_unused_result' [-Wunused-result]
35376 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35489:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
35489 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line':
pysam/libcbcf.c:34915:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34915 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record':
pysam/libcbcf.c:34780:12: warning: ignoring return value of 'bcf_hdr_sync' declared with attribute 'warn_unused_result' [-Wunused-result]
34780 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/bcftools -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -I/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10 -I/usr/include/python3.10 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-gentoo-linux-musl-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/temp.linux-x86_64-3.10/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/pysam -L/usr/lib -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_10/build/lib/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
>>> Source compiled.
>>> Test phase: sci-biology/pysam-0.17.0
 * python3_8: running distutils-r1_run_phase python_test
python3.8 -m pytest -vv -ra -l -Wdefault --color=no -p no:cov -p no:flake8 -p no:flakes -p no:pylint --deselect tests/tabix_test.py::TestRemoteFileHTTP --deselect tests/tabix_test.py::TestRemoteFileHTTPWithHeader
============================= test session starts ==============================
platform linux -- Python 3.8.13, pytest-7.1.1, pluggy-1.0.0 -- /usr/bin/python3.8
cachedir: .pytest_cache
rootdir: /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8, configfile: setup.cfg, testpaths: pysam, tests
collecting ... collected 944 items / 4 deselected / 940 selected

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tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
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tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
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tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp___enter___bahqcd6pnegative_integers.bam'
PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
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tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
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tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
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tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
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tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
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tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
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tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_cjb1ujly'
/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_cjb1ujly
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_ad06xya7'
/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_ad06xya7
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_wcfa4q6h
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_qcs4cfcu'
/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_qcs4cfcu
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_gme1f2sd'
/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_gme1f2sd
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/tmp/pysamtests_tmp_check_read_write_4vg2x9ev
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
Fatal Python error: Segmentation fault

Current thread 0x00007f61b4a17b08 (most recent call first):
  File "/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8/tests/AlignmentFile_test.py", line 55 in tearDown
  File "/usr/lib/python3.8/unittest/case.py", line 636 in _callTearDown
  File "/usr/lib/python3.8/unittest/case.py", line 679 in run
  File "/usr/lib/python3.8/unittest/case.py", line 736 in __call__
  File "/usr/lib/python3.8/site-packages/_pytest/unittest.py", line 327 in runtest
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 166 in pytest_runtest_call
  File "/usr/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 259 in <lambda>
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 338 in from_call
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 258 in call_runtest_hook
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 219 in call_and_report
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 130 in runtestprotocol
  File "/usr/lib/python3.8/site-packages/_pytest/runner.py", line 111 in pytest_runtest_protocol
  File "/usr/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.8/site-packages/_pytest/main.py", line 347 in pytest_runtestloop
  File "/usr/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.8/site-packages/_pytest/main.py", line 322 in _main
  File "/usr/lib/python3.8/site-packages/_pytest/main.py", line 268 in wrap_session
  File "/usr/lib/python3.8/site-packages/_pytest/main.py", line 315 in pytest_cmdline_main
  File "/usr/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/lib/python3.8/site-packages/_pytest/config/__init__.py", line 164 in main
  File "/usr/lib/python3.8/site-packages/_pytest/config/__init__.py", line 187 in console_main
  File "/usr/lib/python3.8/site-packages/pytest/__main__.py", line 5 in <module>
  File "/usr/lib/python3.8/runpy.py", line 87 in _run_code
  File "/usr/lib/python3.8/runpy.py", line 194 in _run_module_as_main
/var/tmp/portage/sci-biology/pysam-0.17.0/temp/environment: line 1867:  6062 Segmentation fault      "${@}"
 * ERROR: sci-biology/pysam-0.17.0::gentoo failed (test phase):
 *   pytest failed with python3.8
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_test
 *   environment, line 3188:  Called distutils-r1_src_test
 *   environment, line 1490:  Called _distutils-r1_run_foreach_impl 'python_test'
 *   environment, line  604:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2851:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2380:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 2378:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test'
 *   environment, line  942:  Called distutils-r1_run_phase 'python_test'
 *   environment, line 1417:  Called python_test
 *   environment, line 3155:  Called distutils-r1_python_test
 *   environment, line 1369:  Called epytest
 *   environment, line 1891:  Called die
 * The specific snippet of code:
 *       "${@}" || die -n "pytest failed with ${EPYTHON}";
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/pysam-0.17.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/pysam-0.17.0::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-biology/pysam-0.17.0:20220405-083315.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/pysam-0.17.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/pysam-0.17.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0-python3_8'
 * S: '/var/tmp/portage/sci-biology/pysam-0.17.0/work/pysam-0.17.0'