build.log

build.log (text/plain), 59.89 KB, created by Agostino Sarubbo on 2023-02-27 10:11:36 UTC

 * Package:    sci-biology/abyss-2.3.4:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux openmp userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox 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/7cfafa107a41c4e2a9933c570465a007ae823593  (Mon Feb 27 02:32:00 UTC 2023)
@@@@@ END @@@@@



##################
# emerge --info: #
##################
Portage 3.0.45 (python 3.11.2-final-0, default/linux/amd64/17.0/musl/hardened, gcc-12, musl-1.2.3-r7, 5.15.85-gentoo-dist x86_64)
=================================================================
System uname: Linux-5.15.85-gentoo-dist-x86_64-AMD_EPYC_7513_32-Core_Processor-with-libc
KiB Mem:   263532996 total,  23442060 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Mon, 27 Feb 2023 02:32:00 +0000
sh bash 5.2_p15-r2
ld GNU ld (Gentoo 2.40 p2) 2.40.0
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.2_p15-r2::gentoo
dev-lang/perl:             5.36.0-r2::gentoo
dev-lang/python:           3.9.16_p2::gentoo, 3.10.10_p2::gentoo, 3.11.2_p1::gentoo
dev-util/cmake:            3.25.2::gentoo
dev-util/meson:            1.0.0::gentoo
sys-apps/baselayout:       2.13-r1::gentoo
sys-apps/openrc:           0.46::gentoo
sys-apps/sandbox:          2.30-r1::gentoo
sys-devel/autoconf:        2.71-r5::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.40-r2::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           16.0.0_rc3::gentoo
sys-devel/gcc:             12.2.1_p20230121-r1::gentoo
sys-devel/gcc-config:      2.10::gentoo
sys-devel/libtool:         2.4.7-r1::gentoo
sys-devel/llvm:            16.0.0_rc3::gentoo
sys-devel/make:            4.4.1::gentoo
sys-kernel/linux-headers:  6.2::gentoo (virtual/os-headers)
sys-libs/musl:             1.2.3-r7::gentoo
Repositories:

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

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* GPL-3"
CBUILD="x86_64-gentoo-linux-musl"
CC="clang"
CFLAGS="-O2 -march=x86-64 -pipe -pipe -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"
CXX="clang++"
CXXFLAGS="-O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0"
DISTDIR="/var/tmp/portage/sci-biology/abyss-2.3.4/distdir"
EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE 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 XDG_STATE_HOME"
FCFLAGS="-O2 -march=x86-64 -pipe -pipe -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 unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=x86-64 -pipe -pipe -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"
LEX="flex"
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 cet cli crypt debug dri elogind fortran hardened iconv ipv6 jumbo-build libglvnd libtirpc native-symlinks ncurses nls nptl openmp pam pcre pie readline seccomp split-usr ssl ssp test-rust unicode xattr xtpax zlib" ABI_X86="64" ELIBC="musl" KERNEL="linux" USERLAND="GNU"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, LC_ALL, LD, 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): #
##############################
2023-02-27T03:08:07 >>> sys-apps/hwdata-0.367
2023-02-27T03:08:08 >>> dev-util/b2-4.9.3-r1
2023-02-27T03:08:11 >>> virtual/fortran-0-r1
2023-02-27T03:08:13 >>> dev-cpp/sparsehash-2.0.4
2023-02-27T03:08:15 >>> x11-libs/libpciaccess-0.17
2023-02-27T03:08:18 >>> dev-libs/boost-1.81.0-r1
2023-02-27T03:08:21 >>> sys-apps/pciutils-3.9.0
2023-02-27T03:08:31 >>> sys-apps/hwloc-2.9.0
2023-02-27T03:08:35 >>> sys-cluster/openmpi-4.1.4-r1




#######################################
# 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/floppy-0:0
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/root-0:0
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/usb-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-r1:0 -pkgcore
app-alternatives/awk-4:0 -busybox gawk -mawk -nawk split-usr
app-alternatives/bzip2-1:0 -lbzip2 -pbzip2 reference split-usr
app-alternatives/gzip-0:0 -pigz reference split-usr
app-alternatives/lex-0-r1:0 flex -reflex
app-alternatives/sh-0:0 bash -busybox -dash -ksh -lksh -mksh
app-alternatives/tar-0:0 gnu -libarchive split-usr
app-alternatives/yacc-1-r2:0 bison -byacc -reference
app-arch/bzip2-1.0.8-r4:0/1 -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 -verify-sig
app-arch/gzip-1.12-r4:0 -pic -static -verify-sig
app-arch/libarchive-3.6.1-r1:0/13 -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-r2:0 acl -minimal nls -selinux -verify-sig xattr
app-arch/unzip-6.0_p27-r1:0 bzip2 -natspec unicode
app-arch/xz-utils-5.4.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 extra-filters nls split-usr -static-libs -verify-sig
app-arch/zstd-1.5.4-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 -lz4 lzma split-usr -static-libs -test zlib
app-crypt/gnupg-2.4.0:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -tpm -usb -user-socket -verify-sig -wks-server
app-crypt/gpgme-1.18.0-r2:1/11.6.15.1 -common-lisp cxx -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -qt5 -static-libs -test -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-1.2.1-r1:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5 -verify-sig
app-crypt/rhash-1.4.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug nls ssl -static-libs
app-editors/nano-7.2:0 -debug -justify -magic -minimal ncurses nls spell -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-r1:0
app-misc/ca-certificates-20211016.3.88.1:0 -cacert
app-misc/editor-wrapper-4-r1:0
app-misc/mime-types-2.1.53:0 -nginx
app-misc/pax-utils-1.3.7:0 -caps -man -python python_single_target_python3_10 -python_single_target_python3_11 -python_single_target_python3_9 -seccomp -test
app-misc/tmux-3.3a-r1:0 debug -selinux -systemd -utempter -vim-syntax
app-portage/eix-0.36.6:0 debug -doc nls -sqlite
app-portage/elt-patches-20221210:0
app-portage/gemato-19.0:0 gpg -pretty-log -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test -tools
app-portage/gentoolkit-0.6.1-r3:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
app-portage/portage-utils-0.95:0 openmp qmanifest qtegrity -static
app-shells/bash-5.2_p15-r2:0 -afs -bashlogger -examples -mem-scramble net nls -pgo -plugins readline -verify-sig
app-shells/bash-completion-2.11:0 eselect -test
app-shells/gentoo-bashcomp-20190211-r1:0
app-shells/push-3.4:0
app-shells/quoter-4.2:0
app-text/ansifilter-2.18:0 -qt5
app-text/build-docbook-catalog-2.3-r1:0
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-ns-stylesheets-1.79.1:0 -ruby
app-text/docbook-xsl-stylesheets-1.79.1-r3:0 -ruby
app-text/manpager-1:0
app-text/sgml-common-0.6.3-r7:0
app-text/xmlto-0.0.28-r10:0 -latex text
dev-cpp/sparsehash-2.0.4:0
dev-db/sqlite-3.41.0:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 debug -doc -icu readline -secure-delete -static-libs -tcl -test -tools
dev-lang/perl-5.36.0-r2:0/5.36 -berkdb debug -doc -gdbm ithreads -minimal -quadmath
dev-lang/python-3.11.2_p1:3.11 -bluetooth -build ensurepip -examples gdbm hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig
dev-lang/python-3.10.10_p2:3.10 -bluetooth -build ensurepip -examples gdbm hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml
dev-lang/python-3.9.16_p2:3.9 -bluetooth -build ensurepip -examples gdbm hardened -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml
dev-lang/python-exec-2.4.10:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-lang/python-exec-conf-2.4.6:2 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-lang/tcl-8.6.13-r1:0/8.6 -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/boehm-gc-8.2.2-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 -cxx large -static-libs threads
dev-libs/boost-1.81.0-r1:0/1.81.0 -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 -context debug -doc -icu -lzma -mpi nls -numpy -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -tools zlib -zstd
dev-libs/elfutils-0.188:0 -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 utils -valgrind -verify-sig -zstd
dev-libs/expat-2.5.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -examples -static-libs unicode
dev-libs/glib-2.74.6:2 -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 -gtk-doc mime -selinux -static-libs -sysprof -systemtap -test -utils xattr
dev-libs/gmp-6.2.1-r5:0/10.4 -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 cpudetection cxx -doc -pic -static-libs
dev-libs/gobject-introspection-1.74.0:0 -doctool -gtk-doc python_single_target_python3_10 -python_single_target_python3_11 -python_single_target_python3_9 -test
dev-libs/gobject-introspection-common-1.74.0:0
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/libatomic_ops-7.6.14:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
dev-libs/libbsd-0.11.7-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 -verify-sig
dev-libs/libevent-2.1.12-r1:0/2.1-7 -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 -verbose-debug
dev-libs/libffi-3.4.4:0/8 -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-r3:0/20 -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 getentropy -static-libs -verify-sig
dev-libs/libgpg-error-1.46-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 -common-lisp nls -static-libs -test -verify-sig
dev-libs/libksba-1.6.3:0 -static-libs -verify-sig
dev-libs/libltdl-2.4.7-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 -static-libs
dev-libs/libpcre2-10.42-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 -verify-sig zlib
dev-libs/libpipeline-1.5.7:0 -test
dev-libs/libtasn1-4.19.0:0/6 -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 -verify-sig
dev-libs/libunistring-1.1-r1:0/5 -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-1.44.2-r1:0/1
dev-libs/libxml2-2.10.3-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 ftp -icu -lzma python python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 readline -static-libs -test
dev-libs/libxslt-1.1.37-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 crypt debug -examples -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -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-1.3.1:0/3 -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-4.2.0:0/6 -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 -verify-sig
dev-libs/nettle-3.8.1:0/8-6 -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_aes -cpu_flags_arm_neon -cpu_flags_arm_sha1 -cpu_flags_arm_sha2 -cpu_flags_ppc_altivec cpu_flags_x86_aes cpu_flags_x86_pclmul -cpu_flags_x86_sha -doc gmp -static-libs -verify-sig
dev-libs/npth-1.6-r1:0 -test
dev-libs/openssl-3.0.8:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 asm cpu_flags_x86_sse2 -fips -ktls -rfc3779 -sctp -static-libs -test -tls-compression -vanilla -verify-sig -verify-sig -weak-ssl-ciphers
dev-libs/popt-1.19:0 -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/Clone-0.460.0:0 -test
dev-perl/Devel-CheckLib-1.160.0:0 -test
dev-perl/Encode-Locale-1.50.0-r1:0 -test
dev-perl/File-BaseDir-0.90.0:0 -test
dev-perl/File-DesktopEntry-0.220.0-r1:0 -test
dev-perl/File-Listing-6.150.0:0 -test -test
dev-perl/File-MimeInfo-0.300.0:0 -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-6.440.0:0 -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-2.81.0:0 -examples -idn -test
dev-perl/IPC-System-Simple-1.300.0:0 -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-1.920.0:0 -examples -examples -minimal -test
dev-perl/Socket6-0.290.0:0 -test
dev-perl/Sub-Name-0.260.0:0 -suggested -test
dev-perl/TimeDate-2.330.0-r1:0 -test
dev-perl/Try-Tiny-0.310.0:0 -minimal -test
dev-perl/URI-5.110.0:0 -test
dev-perl/WWW-RobotRules-6.20.0-r2:0 -test
dev-perl/XML-Parser-2.460.0-r2:0
dev-python/alabaster-0.7.13:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-python/autocommand-2.2.2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/Babel-2.11.0:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/certifi-3021.3.16-r3:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/charset_normalizer-3.0.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/cython-0.29.33:0 -doc -emacs -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/docutils-0.19:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-python/ensurepip-pip-23.0.1:0
dev-python/ensurepip-setuptools-67.4.0:0
dev-python/ensurepip-wheels-100:0
dev-python/flit_core-3.8.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/gentoo-common-1:0
dev-python/gpep517-13:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/idna-3.4:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/imagesize-1.4.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/importlib_metadata-6.0.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/inflect-6.0.2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/installer-0.6.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/jaraco-context-4.3.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/jaraco-functools-3.6.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/jaraco-text-3.11.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/jinja-3.1.2:0 -doc -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/markupsafe-2.1.2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/more-itertools-9.0.0:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/nspektr-0.4.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/ordered-set-4.1.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/packaging-23.0-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/platformdirs-3.0.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/pydantic-1.10.5:0 native-extensions -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/pygments-2.14.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/pyparsing-3.0.9:0 -examples -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/pypax-0.9.5-r1:0 -ptpax python_targets_python3_10 python_targets_python3_9 xtpax
dev-python/PySocks-1.7.1-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-python/pytz-2022.7.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-python/requests-2.28.2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -socks5 -test test-rust
dev-python/setuptools-67.4.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/setuptools_scm-7.1.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/six-1.16.0-r1:0 -doc -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/snowballstemmer-2.2.0-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-python/sphinx-6.1.3:0 -doc -latex -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/sphinxcontrib-applehelp-1.0.4:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/sphinxcontrib-devhelp-1.0.2-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/sphinxcontrib-htmlhelp-2.0.1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/sphinxcontrib-jsmath-1.0.1-r2:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/sphinxcontrib-qthelp-1.0.3-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/sphinxcontrib-serializinghtml-1.1.5-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/tomli-2.0.1-r1:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/typing-extensions-4.5.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/urllib3-1.26.14:0 -brotli -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/wheel-0.38.4:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-python/zipp-3.15.0:0 -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-util/b2-4.9.3-r1:0 -examples
dev-util/checkbashisms-2.22.2:0
dev-util/cmake-3.25.2:0 -doc -emacs ncurses -qt5 -test -test -verify-sig
dev-util/desktop-file-utils-0.26-r2:0 -emacs
dev-util/glib-utils-2.74.6:0 python_single_target_python3_10 -python_single_target_python3_11 -python_single_target_python3_9
dev-util/gperf-3.1-r1:0
dev-util/gtk-doc-am-1.33.2:0
dev-util/intltool-0.51.0-r3:0
dev-util/meson-1.0.0:0 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -test
dev-util/meson-format-array-0:0 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9
dev-util/ninja-1.11.1-r2:0 -doc -emacs -test
dev-util/pkgconf-1.8.1:0/3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -test
dev-util/re2c-2.2:0 debug -test
dev-vcs/git-2.39.2:0 blksha1 -cgi curl -cvs -doc -gnome-keyring gpg -highlight iconv -mediawiki -mediawiki-experimental nls pcre -perforce -perl python_single_target_python3_10 -python_single_target_python3_11 -python_single_target_python3_9 safe-directory -selinux -subversion -test -tk webdav -xinetd
media-fonts/liberation-fonts-2.1.5:0 -X -X -fontforge
media-gfx/graphite2-1.3.14_p20210810-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 -perl -test
media-libs/fontconfig-2.14.2:1.0 -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 nls -test
media-libs/freetype-2.13.0:2 -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-6.0.0:0/6.0.0 -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/libpng-1.6.39:0/16 -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
net-dns/c-ares-1.19.0:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -static-libs -test -verify-sig
net-dns/libidn2-2.3.4:0/2 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 nls -static-libs -verify-sig
net-firewall/iptables-1.8.9:0/1.8.3 -conntrack -netlink -nftables -pcap split-usr -static-libs
net-libs/gnutls-3.8.0:0/30.30 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -brotli cxx -dane -doc -examples idn nls openssl -pkcs11 seccomp -sslv2 -sslv3 -static-libs -test -test-full tls-heartbeat -tools -valgrind -verify-sig zlib -zstd
net-libs/libmnl-1.0.5:0/0.2.0 -examples -verify-sig
net-libs/nghttp2-1.51.0:0/1.14 -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 -utils -xml
net-misc/curl-7.88.1-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 -curl_ssl_rustls ftp -gnutls -gopher -hsts http2 -idn imap -kerberos -ldap -mbedtls -nghttp3 -nss openssl pop3 progress-meter -rtmp -rustls -samba smtp -ssh ssl -sslv3 -static-libs -telnet -test tftp -verify-sig -websockets -zstd
net-misc/dhcpcd-9.4.1:0 debug embedded ipv6 -privsep udev
net-misc/iputils-20221126-r1:0 arping -caps -clockdiff -doc filecaps -idn nls -test -tracepath
net-misc/netifrc-0.7.3-r1:0 dhcp
net-misc/openssh-9.2_p1-r2:0 -X -X509 -abi_mips_n32 -audit -debug -hpn -kerberos -ldns -libedit -livecd pam pie -sctp -security-key -selinux ssl -static -test -verify-sig -xmss
net-misc/rsync-3.2.7-r2:0 acl -examples iconv -lz4 python_single_target_python3_10 -python_single_target_python3_11 -python_single_target_python3_9 -rrsync ssl -stunnel -system-zlib -verify-sig xattr -xxhash -zstd
net-misc/wget-1.21.3-r1:0 -cookie-check debug -gnutls -idn ipv6 -metalink nls -ntlm pcre ssl -static -test -uuid -verify-sig zlib
perl-core/Compress-Raw-Zlib-2.202.0:0
perl-core/File-Temp-0.231.100:0
sec-keys/openpgp-keys-gentoo-release-20220101:0 -test
sys-apps/acl-2.3.1-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 split-usr -static-libs
sys-apps/attr-2.5.1-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 debug nls split-usr -static-libs
sys-apps/baselayout-2.13-r1:0 -build split-usr
sys-apps/coreutils-9.1-r2:0 acl -caps -gmp -hostname -kill -multicall nls openssl -selinux split-usr -static -test -vanilla -verify-sig xattr
sys-apps/dbus-1.15.4:0 -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-3.9-r1:0 nls -static -verify-sig
sys-apps/elfix-0.9.5:0 -ptpax xtpax
sys-apps/file-5.44-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 bzip2 -lzip -lzma -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -seccomp -static-libs -verify-sig zlib -zstd
sys-apps/findutils-4.9.0-r2:0 nls -selinux -static -test -verify-sig
sys-apps/gawk-5.2.1:0 -mpfr nls -pma readline -verify-sig
sys-apps/gentoo-functions-0.19:0
sys-apps/grep-3.8-r1:0 egrep-fgrep nls pcre -static -verify-sig
sys-apps/groff-1.22.4:0 -X -examples -uchardet
sys-apps/help2man-1.49.3:0 nls
sys-apps/hwdata-0.367:0
sys-apps/hwloc-2.9.0:0/15 -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 -cairo cpuid -cuda debug -nvml pci -static-libs -svg -udev -video_cards_nvidia -xml
sys-apps/install-xattr-0.8-r1:0
sys-apps/iproute2-6.2.0:0 -atm -berkdb -bpf -caps -elf iptables -libbsd -minimal -nfs -selinux split-usr
sys-apps/kbd-2.5.1:0 nls pam -test
sys-apps/kmod-30-r1:0 debug -doc lzma -pkcs7 -python python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 -static-libs tools zlib zstd
sys-apps/less-608-r2:0 pcre unicode
sys-apps/man-db-2.11.2:0 manpager -nls seccomp -selinux -static-libs zlib
sys-apps/miscfiles-1.5-r4:0 -minimal
sys-apps/net-tools-2.10:0 arp hostname ipv6 -nis nls -plipconfig -selinux -slattach -static
sys-apps/openrc-0.46:0 -audit -bash debug ncurses netifrc -newnet pam -selinux -sysv-utils unicode
sys-apps/pciutils-3.9.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -dns kmod -static-libs udev zlib
sys-apps/portage-3.0.45:0 -apidoc -build -doc -gentoo-dev ipc native-extensions -python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_9 rsync-verify -selinux -test xattr
sys-apps/sandbox-2.30-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 nnp
sys-apps/sed-4.9:0 acl nls -selinux -static -verify-sig
sys-apps/shadow-4.13-r2:0/4 acl -audit -bcrypt -cracklib nls pam -selinux -skey split-usr -su -verify-sig xattr
sys-apps/systemd-utils-252.6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -boot kmod -selinux split-usr -split-usr -sysusers -test tmpfiles udev
sys-apps/sysvinit-3.06-r1:0 -ibm -nls -selinux -static -verify-sig
sys-apps/texinfo-7.0.2:0 nls standalone -static
sys-apps/util-linux-2.38.1-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 -audit -build -caps cramfs -cryptsetup -fdformat hardlink -kill logger -magic ncurses nls pam -python python_targets_python3_10 python_targets_python3_11 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 -test
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-cluster/openmpi-4.1.4-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 -cma -cuda -cxx fortran ipv6 -java -java -libompitrace -openmpi_fabrics_knem -openmpi_fabrics_ofed -openmpi_ofed_features_control-hdr-padding -openmpi_ofed_features_dynamic-sl -openmpi_ofed_features_rdmacm -openmpi_ofed_features_udcm -openmpi_rm_pbs -openmpi_rm_slurm -peruse -romio
sys-devel/autoconf-2.71-r5:2.71 -emacs
sys-devel/autoconf-archive-2023.02.20:0
sys-devel/autoconf-wrapper-20221207-r1:0
sys-devel/automake-1.16.5:1.16 -test
sys-devel/automake-wrapper-20221207:0
sys-devel/binutils-2.40-r2:2.40 cet -doc -gold -gprofng -multitarget nls -pgo plugins -static-libs -test -vanilla -zstd
sys-devel/binutils-config-5.5:0 native-symlinks
sys-devel/bison-3.8.2-r2:0 -examples nls -static -test -verify-sig
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#######################
# build.log           #
#######################

>>> Unpacking source...
>>> Unpacking abyss-2.3.4.tar.gz to /var/tmp/portage/sci-biology/abyss-2.3.4/work
>>> Source unpacked in /var/tmp/portage/sci-biology/abyss-2.3.4/work
>>> Preparing source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ...
 * Running eautoreconf in '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' ...
 * Running 'aclocal --system-acdir=/var/tmp/portage/sci-biology/abyss-2.3.4/temp/aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --foreign --force-missing' ...
 [ ok ]
 * Running elibtoolize in: abyss-2.3.4/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ...
 * econf: updating abyss-2.3.4/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating abyss-2.3.4/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=x86_64-gentoo-linux-musl --host=x86_64-gentoo-linux-musl --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/abyss-2.3.4 --htmldir=/usr/share/doc/abyss-2.3.4/html --libdir=/usr/lib --enable-openmp --enable-maxk=256
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether clang++ accepts -g... yes
checking for clang++ option to enable C++11 features... none needed
checking whether clang++ supports C++11 features with -std=c++11... yes
checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking whether UID '250' is supported by ustar format... yes
checking whether GID '250' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking dependency style of clang++ -std=c++11... none
checking for gawk... (cached) gawk
checking for x86_64-gentoo-linux-musl-gcc... clang
checking whether the compiler supports GNU C... yes
checking whether clang accepts -g... yes
checking for clang option to enable C11 features... none needed
checking whether clang understands -c and -o together... yes
checking dependency style of clang... none
checking how to run the C preprocessor... clang -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether clang++ -std=c++11 accepts -g... (cached) yes
checking for clang++ -std=c++11 option to enable C++11 features... (cached) none needed
checking for x86_64-gentoo-linux-musl-ranlib... x86_64-gentoo-linux-musl-ranlib
checking for x86_64-gentoo-linux-musl-ghc... no
checking for ghc... (cached) no
./configure: line 7028: : command not found
checking for pandoc... no
checking for x86_64-gentoo-linux-musl-ar... x86_64-gentoo-linux-musl-ar
checking the archiver (x86_64-gentoo-linux-musl-ar) interface... ar
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for vfork.h... no
checking for dlfcn.h... yes
checking for fcntl.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for sys/param.h... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ptrdiff_t... yes
checking for mode_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for std::hash<int>... yes
checking for std::tr1::hash<int>... yes
checking for std::tr1::tuple<int>... yes
checking for dup2... yes
checking for gethostname... yes
checking for getopt_long... yes
checking for getpagesize... yes
checking for memset... yes
checking for strdup... yes
checking for strerror... yes
checking for strtoul... yes
checking for fork... yes
checking for vfork... yes
checking for vprintf... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking build system type... x86_64-gentoo-linux-musl
checking host system type... x86_64-gentoo-linux-musl
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for GNU libc compatible realloc... yes
checking for clang options needed to detect all undeclared functions... none needed
checking whether HOST_NAME_MAX is declared... yes
checking if compiler needs -Werror to reject unknown flags... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for mpi.h... yes
checking for MPI_Init in -lmpi... yes
checking for sqrt in -lm... yes
checking for pow... yes
checking for sqrt... yes
checking for ceilf... yes
checking for dlsym in -ldl... yes
checking for functional... yes
checking for tr1/functional... yes
checking for boost/functional/hash.hpp... yes
checking for boost/property_map/property_map.hpp... yes
checking for google/sparse_hash_map... yes
checking for unordered_map... yes
checking for tr1/unordered_map... yes
checking for unordered_set... yes
checking for tr1/unordered_set... yes
checking for boost/unordered_set.hpp... yes
checking for sqlite3.h... yes
checking for main in -lsqlite3... yes
checking for clang++ -std=c++11 option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating vendor/gtest-1.7.0/Makefile
config.status: creating RResolver/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating vendor/Makefile
config.status: creating config.h
config.status: executing depfiles commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ...
make -j16 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4'
Making all in bin
make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/bin'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/bin'
Making all in doc
make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/doc'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/doc'
Making all in Common
make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/Common'
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
clang++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4      -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra  -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc
In file included from Timer.cpp:1:
./Timer.h:17:3: error: unknown type name 'clock_t'
                clock_t m_start;
                ^
./Timer.h:17:11: warning: private field 'm_start' is not used [-Wunused-private-field]
                clock_t m_start;
                        ^
1 warning and 1 error generated.
make[2]: *** [Makefile:558: libcommon_a-Timer.o] Error 1
make[2]: *** Waiting for unfinished jobs....
Uncompress.cpp:160:7: error: redefinition of 'fopen'
FILE *fopen64(const char *path, const char *mode)
      ^
/usr/include/stdio.h:210:17: note: expanded from macro 'fopen64'
#define fopen64 fopen
                ^
Uncompress.cpp:133:7: note: previous definition is here
FILE *fopen(const char *path, const char *mode)
      ^
Uncompress.cpp:184:52: error: unknown type name 'mode_t'
typedef int (*open_t)(const char *path, int flags, mode_t mode);
                                                   ^
Uncompress.cpp:189:39: error: unknown type name 'mode_t'
int open(const char *path, int flags, mode_t mode)
                                      ^
3 errors generated.
make[2]: *** [Makefile:572: libcommon_a-Uncompress.o] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/Common'
make[1]: *** [Makefile:488: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4'
make: *** [Makefile:408: all] Error 2
 * ERROR: sci-biology/abyss-2.3.4::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/abyss-2.3.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-2.3.4::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-biology/abyss-2.3.4:20230227-030842.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/abyss-2.3.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/abyss-2.3.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4'
 * S: '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4'