build.log

build.log (text/plain), 109.11 KB, created by Agostino Sarubbo on 2022-07-30 19:14:38 UTC

 * Package:    sci-chemistry/mdtraj-1.9.7
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 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/33a91adb9b42001439a74e88b4b4cf8c0a9b306d  (Sat Jul 30 18:01:49 UTC 2022)
@@@@@ END @@@@@



##################
# emerge --info: #
##################
Portage 3.0.34 (python 3.10.5-final-0, default/linux/amd64/17.1, gcc-12.1.1, glibc-2.35-r8, 5.10.133-gentoo x86_64)
=================================================================
System uname: Linux-5.10.133-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-glibc2.35
KiB Mem:   264024340 total, 234465464 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sat, 30 Jul 2022 18:01:48 +0000
sh bash 5.1_p16
ld GNU ld (Gentoo 2.38 p4) 2.38
app-misc/pax-utils:        1.3.4::gentoo
app-shells/bash:           5.1_p16::gentoo
dev-lang/perl:             5.36.0::gentoo
dev-lang/python:           3.8.13_p2::gentoo, 3.9.13::gentoo, 3.10.5::gentoo, 3.11.0_beta5::gentoo
dev-util/cmake:            3.23.3::gentoo
dev-util/meson:            0.63.0::gentoo
sys-apps/baselayout:       2.8-r2::gentoo
sys-apps/openrc:           0.45.2::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-r2::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/gcc:             12.1.1_p20220625::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:  5.18-r1::gentoo (virtual/os-headers)
sys-libs/glibc:            2.35-r8::gentoo
Repositories:

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

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* GPL-2"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing"
CHOST="x86_64-pc-linux-gnu"
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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing"
DISTDIR="/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing"
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 multilib-strict 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 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing"
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"
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 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl unicode xattr zlib" ABI_X86="64" ELIBC="glibc" 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, INSTALL_MASK, 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): #
##############################
2022-07-30T20:00:49 >>> sci-libs/suitesparseconfig-5.4.0
2022-07-30T20:00:54 >>> app-eselect/eselect-lapack-0.2
2022-07-30T20:00:51 >>> dev-lang/swig-4.0.2
2022-07-30T20:00:52 >>> app-eselect/eselect-blas-0.2
2022-07-30T20:00:56 >>> virtual/fortran-0-r1
2022-07-30T20:00:57 >>> dev-util/patchelf-0.15.0
2022-07-30T20:01:02 >>> app-arch/lz4-1.9.3-r1
2022-07-30T20:01:00 >>> media-libs/libjpeg-turbo-2.1.3
2022-07-30T20:01:03 >>> dev-cpp/eigen-3.4.0-r1
2022-07-30T20:01:06 >>> app-arch/snappy-1.1.9-r1
2022-07-30T20:01:05 >>> sci-libs/metis-5.1.0-r5
2022-07-30T20:01:10 >>> dev-python/gast-0.5.3-r1
2022-07-30T20:01:08 >>> dev-python/cython-0.29.32
2022-07-30T20:01:13 >>> dev-python/astunparse-1.6.3
2022-07-30T20:01:17 >>> dev-python/pyproject-metadata-0.6.1
2022-07-30T20:01:15 >>> dev-python/networkx-2.8.5
2022-07-30T20:01:19 >>> dev-python/ply-3.11-r2
2022-07-30T20:01:20 >>> dev-python/olefile-0.46-r2
2022-07-30T20:01:22 >>> dev-python/python-dateutil-2.8.2-r1
2022-07-30T20:01:24 >>> dev-python/pytz-2022.1
2022-07-30T20:01:25 >>> dev-lang/nasm-2.15.05
2022-07-30T20:01:27 >>> dev-python/astor-0.8.1-r1
2022-07-30T20:01:39 >>> sci-libs/colamd-2.9.6
2022-07-30T20:01:43 >>> sci-libs/camd-2.4.6-r1
2022-07-30T20:01:41 >>> sci-libs/ccolamd-2.9.6
2022-07-30T20:02:13 >>> sci-libs/lapack-3.10.1
2022-07-30T20:02:13 >>> sci-libs/amd-2.4.6-r1
2022-07-30T20:02:34 >>> dev-python/pybind11-2.10.0
2022-07-30T20:02:16 >>> sci-libs/hdf5-1.12.2-r4
2022-07-30T20:02:39 >>> dev-libs/c-blosc-1.21.1
2022-07-30T20:02:48 >>> dev-python/beniget-0.4.1-r1
2022-07-30T20:03:12 >>> dev-python/meson-python-0.8.1
2022-07-30T20:03:49 >>> media-libs/tiff-4.4.0
2022-07-30T20:04:25 >>> virtual/blas-3.8
2022-07-30T20:04:24 >>> virtual/cblas-3.8
2022-07-30T20:04:21 >>> virtual/lapack-3.10
2022-07-30T20:04:57 >>> dev-python/pillow-9.2.0
2022-07-30T20:05:16 >>> sci-libs/arpack-3.8.0
2022-07-30T20:05:18 >>> sci-libs/cholmod-3.0.14
2022-07-30T20:05:20 >>> dev-python/numpy-1.23.1
2022-07-30T20:05:34 >>> sci-libs/umfpack-5.7.9
2022-07-30T20:05:46 >>> dev-python/pythran-0.11.0
2022-07-30T20:05:48 >>> dev-python/bottleneck-1.3.5
2022-07-30T20:05:44 >>> dev-python/numexpr-2.8.3
2022-07-30T20:06:13 >>> dev-python/scipy-1.9.0
2022-07-30T20:06:22 >>> dev-python/pytables-3.7.0
2022-07-30T20:06:24 >>> dev-python/pandas-1.4.3




#######################################
# 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/polkitd-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/polkitd-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 -verify-sig
app-arch/gzip-1.12:0 -pic -static -verify-sig
app-arch/libarchive-3.6.1:0/13 -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/lz4-1.9.3-r1:0/r132 -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
app-arch/snappy-1.1.9-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 -test
app-arch/tar-1.34:0 acl -minimal nls -selinux -verify-sig xattr
app-arch/unzip-6.0_p26:0 bzip2 -natspec unicode
app-arch/xz-utils-5.2.5-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 extra-filters nls split-usr -static-libs -verify-sig
app-arch/zstd-1.5.2-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 -lz4 split-usr -static-libs threads
app-crypt/gnupg-2.3.7-r1:0 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-r1:1/11.6.15 -common-lisp cxx -python python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 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-1.2.0-r1:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5
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-6.3:0 -debug -justify -magic -minimal ncurses nls spell split-usr -static unicode
app-eselect/eselect-blas-0.2:0
app-eselect/eselect-fontconfig-20220403:0
app-eselect/eselect-iptables-20220320:0
app-eselect/eselect-lapack-0.2:0
app-eselect/eselect-lib-bin-symlink-0.1.1-r1:0
app-eselect/eselect-pinentry-0.7.2:0
app-i18n/man-pages-ja-20180315-r1:0
app-i18n/man-pages-l10n-4.14.0-r1:0 l10n_cs l10n_da l10n_de l10n_el l10n_es l10n_fi l10n_fr l10n_hu l10n_id l10n_it l10n_mk l10n_nb l10n_nl l10n_pl l10n_pt-BR l10n_ro l10n_sr l10n_sv l10n_uk l10n_vi
app-i18n/man-pages-ru-5.03.2390.2390.20191017-r1:0
app-i18n/man-pages-zh_CN-1.6.3.6:0
app-misc/c_rehash-1.7-r1:0
app-misc/ca-certificates-20211016.3.80:0 -cacert
app-misc/editor-wrapper-4-r1:0
app-misc/mime-types-2.1.53:0 -nginx
app-misc/pax-utils-1.3.4:0 -caps -debug -python python_single_target_python3_10 -python_single_target_python3_8 -python_single_target_python3_9 seccomp
app-misc/tmux-3.3a:0 -debug -selinux -systemd -utempter -vim-syntax
app-portage/eix-0.36.4:0 -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_11 python_targets_python3_8 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_8 python_targets_python3_9 -test
app-portage/portage-utils-0.94.1:0 nls openmp qmanifest qtegrity -static
app-shells/bash-5.1_p16:0 -afs -bashlogger -examples -mem-scramble net nls -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-stylesheets-1.79.1-r3:0 -ruby
app-text/manpager-1:0
app-text/opensp-1.5.2-r7:0 -doc nls -static-libs -test
app-text/po4a-0.66:0 -test -test
app-text/sgml-common-0.6.3-r7:0
app-text/xmlto-0.0.28-r8:0 -latex text
dev-cpp/eigen-3.4.0-r1:3 -cpu_flags_arm_neon -cpu_flags_ppc_altivec -cpu_flags_ppc_vsx -cuda -debug -doc openmp -test
dev-db/sqlite-3.39.2:3 -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/duktape-2.7.0-r1:0/2.7.0
dev-lang/nasm-2.15.05:0 -doc
dev-lang/perl-5.36.0:0/5.36 -berkdb -debug -doc gdbm ithreads -minimal -quadmath
dev-lang/python-3.11.0_beta5:3.11 -bluetooth -build -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst
dev-lang/python-3.10.5:3.10 -bluetooth -build -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml
dev-lang/python-3.9.13:3.9 -bluetooth -build -examples gdbm -hardened -lto ncurses -pgo readline sqlite ssl -test -tk -verify-sig -wininst xml
dev-lang/python-3.8.13_p2:3.8 -bluetooth -build -examples gdbm -hardened ncurses readline sqlite ssl -test -tk -verify-sig -wininst xml
dev-lang/python-exec-2.4.9:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 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_11 python_targets_python3_8 python_targets_python3_9
dev-lang/swig-4.0.2:0 -ccache -doc pcre
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/boehm-gc-8.0.6:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cxx large -static-libs threads
dev-libs/c-blosc-1.21.1:0/1 lz4 snappy -test zlib -zstd
dev-libs/elfutils-0.187:0 -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 -verify-sig -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-2.72.3:2 -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/libatomic_ops-7.6.12:0 -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-0.11.6:0 -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-r2:0/8 -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 -experimental-loong -pax-kernel -static-libs -test
dev-libs/libffi-compat-3.3-r2:7 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -pax-kernel -test
dev-libs/libgcrypt-1.10.1-r1:0/20 -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 -static-libs -verify-sig
dev-libs/libgpg-error-1.45:0 -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
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/libpcre2-10.40:0/3 -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-1.5.6:0 -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-1.44.2:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32
dev-libs/libxml2-2.9.14-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_11 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-3.8.1:0/8-6 -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-1.1.1q: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 -weak-ssl-ciphers
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-EUCJPASCII-0.30.0-r1:0 -test
dev-perl/Encode-HanExtra-0.230.0-r3:0
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-6.330.0:0 -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/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/MIME-Charset-1.12.2-r1:0 l10n_ja l10n_zh -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/Pod-Parser-1.630.0-r1:0 -test
dev-perl/SGMLSpm-1.1-r2:0 -test
dev-perl/Socket6-0.290.0:0 -test
dev-perl/Sub-Name-0.260.0:0 -suggested -test
dev-perl/TermReadKey-2.380.0:0 -examples -test
dev-perl/Text-CharWidth-0.40.0-r2:0 -test
dev-perl/Text-WrapI18N-0.60.0-r2:0 -test
dev-perl/TimeDate-2.330.0-r1:0 -test
dev-perl/Try-Tiny-0.310.0:0 -minimal -test
dev-perl/Unicode-LineBreak-2019.1.0:0
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-perl/YAML-Tiny-1.730.0-r1:0 -minimal -test
dev-python/appdirs-1.4.4-r2:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
dev-python/astor-0.8.1-r1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/astunparse-1.6.3:0 python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/beniget-0.4.1-r1:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/bottleneck-1.3.5:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/certifi-3021.3.16-r2:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/charset_normalizer-2.1.0:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/cython-0.29.32:0 -doc -emacs python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 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_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/gast-0.5.3-r1:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/gpep517-9:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/idna-3.3-r1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/importlib_metadata-4.12.0:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/importlib_resources-5.9.0:0 python_targets_pypy3 python_targets_python3_8 -test
dev-python/installer-0.5.1-r1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jaraco-context-4.1.2:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jaraco-functools-3.5.1:0 -doc python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/jaraco-text-3.8.1:0 -doc python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 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_8 python_targets_python3_9 -test
dev-python/markupsafe-2.1.1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/meson-python-0.8.1:0 -doc python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/more-itertools-8.13.0:0 -doc python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/networkx-2.8.5:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test -test
dev-python/nspektr-0.4.0:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/numexpr-2.8.3:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
dev-python/numpy-1.23.1:0 -doc lapack python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/olefile-0.46-r2:0 -doc python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 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_11 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_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pandas-1.4.3:0 -X -doc -full-support -minimal python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pillow-9.2.0:0 -examples -imagequant jpeg -jpeg2k -lcms python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test -test tiff -tk truetype -webp -xcb zlib
dev-python/ply-3.11-r2:0/3.11 -examples python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
dev-python/pybind11-2.10.0:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 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_8 python_targets_python3_9 -test
dev-python/pyproject-metadata-0.6.1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pypy3-7.3.9_p3:0/pypy39-pp73-336 bzip2 gdbm jit ncurses -sqlite -test -tk
dev-python/pypy3-exe-bin-7.3.9_p3:3.9-7.3.9
dev-python/PySocks-1.7.1-r2:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
dev-python/pytables-3.7.0:0 -examples python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 -test
dev-python/python-dateutil-2.8.2-r1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/pythran-0.11.0:0 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_11 python_targets_python3_8 python_targets_python3_9
dev-python/requests-2.28.1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -socks5 -test
dev-python/scipy-1.9.0:0 -doc python_targets_python3_10 python_targets_python3_8 python_targets_python3_9 sparse -test
dev-python/setuptools-63.2.0:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/setuptools_scm-7.0.5:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 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_8 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_8 python_targets_python3_9 -test
dev-python/typing-extensions-4.3.0:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
dev-python/urllib3-1.26.11:0 -brotli python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 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_11 python_targets_python3_8 python_targets_python3_9 -test
dev-python/zipp-3.8.1:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-util/checkbashisms-2.22.2:0
dev-util/cmake-3.23.3:0 -doc -emacs ncurses -qt5 -test -test -verify-sig
dev-util/desktop-file-utils-0.26-r2:0 -emacs
dev-util/glib-utils-2.72.3:0 python_single_target_python3_10 -python_single_target_python3_11 -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-r3:0
dev-util/meson-0.63.0:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test
dev-util/meson-format-array-0:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
dev-util/ninja-1.11.0:0 -doc -emacs -test -vim-syntax
dev-util/patchelf-0.15.0:0
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 -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 -selinux -subversion -test threads -tk webdav -xinetd
media-fonts/liberation-fonts-2.1.3:0 -X -X -fontforge
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-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-2.12.1:2 -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-5.0.1:0/4.0.0 -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/tiff-4.4.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 cxx -jbig jpeg -lzma -static-libs -test -verify-sig -webp zlib -zstd
net-dns/libidn2-2.3.3:0/2 -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-1.8.8-r4:0/1.8.3 -conntrack -netlink -nftables -pcap split-usr -static-libs
net-libs/gnutls-3.7.7:0/30.30 -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 -guile 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/libnsl-2.0.0-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 -static-libs
net-libs/libtirpc-1.3.2-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 ipv6 -kerberos split-usr -static-libs
net-libs/nghttp2-1.48.0:0/1.14 -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-7.84.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -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 -verify-sig -zstd
net-misc/dhcpcd-9.4.1:0 -debug embedded ipv6 -privsep udev
net-misc/iputils-20211215:0 arping -caps -clockdiff -doc filecaps -idn nls -rarpd -rdisc -static -test -tracepath
net-misc/netifrc-0.7.3-r1:0 dhcp
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sys-devel/gnuconfig-20220508:0
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sys-fs/udev-init-scripts-35:0
sys-kernel/installkernel-gentoo-5:0 -grub
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sys-libs/ncurses-6.3_p20220423-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 -ada cxx -debug -doc -gpm -minimal -profile split-usr stack-realign -static-libs -test tinfo -trace -verify-sig
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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 -verify-sig
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
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virtual/awk-1:0
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virtual/cblas-3.8:0 -eselect-ldso
virtual/dev-manager-0-r2:0
virtual/editor-0-r3:0
virtual/fortran-0-r1:0 openmp
virtual/lapack-3.10:0 -eselect-ldso
virtual/libc-1-r1:0
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virtual/libelf-3-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
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-r7:0/1 -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
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virtual/perl-Carp-1.520.0-r2:0
virtual/perl-Compress-Raw-Bzip2-2.103.0-r2:0
virtual/perl-Compress-Raw-Zlib-2.202.0:0
virtual/perl-CPAN-2.330.0:0
virtual/perl-CPAN-Meta-2.150.10-r6:0
virtual/perl-CPAN-Meta-Requirements-2.140.0-r8:0
virtual/perl-CPAN-Meta-YAML-0.18.0-r8:0
virtual/perl-Data-Dumper-2.184.0:0
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virtual/perl-Encode-3.170.0:0
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virtual/perl-ExtUtils-CBuilder-0.280.236-r1:0
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virtual/perl-ExtUtils-Manifest-1.730.0-r1:0
virtual/perl-ExtUtils-ParseXS-3.450.0:0
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virtual/perl-File-Spec-3.840.0:0
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virtual/perl-Getopt-Long-2.520.0-r1:0
virtual/perl-IO-1.500.0:0
virtual/perl-IO-Compress-2.106.0:0
virtual/perl-IO-Socket-IP-0.410.0-r1:0
virtual/perl-JSON-PP-4.70.0:0
virtual/perl-libnet-3.140.0:0 ssl
virtual/perl-MIME-Base64-3.160.0-r1:0
virtual/perl-Module-Metadata-1.0.37-r2:0
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virtual/perl-Perl-OSType-1.10.0-r6:0
virtual/perl-podlators-4.140.0-r3:0
virtual/perl-Scalar-List-Utils-1.620.0:0
virtual/perl-Test-Harness-3.440.0:0
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virtual/tmpfiles-0-r3:0
virtual/ttf-fonts-1-r1:0
virtual/udev-217-r5:0
virtual/w3m-1:0
virtual/yacc-0:0
www-client/pybugz-0.13-r2:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9
www-client/w3m-0.5.3_p20220429:0 -X -fbcon -gdk-pixbuf -gpm -imlib l10n_ja -lynxkeymap nls -nntp ssl unicode -xface
x11-apps/xprop-1.2.5:0
x11-apps/xset-1.2.4-r1:0
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x11-libs/libICE-1.0.10-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 ipv6
x11-libs/libSM-1.2.3-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 -doc ipv6 uuid
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x11-misc/compose-tables-1.8.1:0
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#######################
# build.log           #
#######################
>>> Unpacking source...
>>> Unpacking mdtraj-1.9.7.tar.gz to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ...
 * Build system packages:
 *   dev-python/setuptools         : 63.2.0
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7 ...
 * python3_8: running distutils-r1_run_phase distutils-r1_python_compile
python3.8 setup.py build -j 16
Using built-in specs.
COLLECT_GCC=x86_64-pc-linux-gnu-gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/12.1.1/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-12.1.1_p20220625/work/gcc-12-20220625/configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/12.1.1 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/12.1.1/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/12.1.1 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/12.1.1/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/12.1.1/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/12.1.1/include/g++-v12 --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/12.1.1/python --enable-languages=c,c++,fortran --enable-obsolete --enable-secureplt --disable-werror --with-system-zlib --enable-nls --without-included-gettext --disable-libunwind-exceptions --enable-checking=release --with-bugurl=https://bugs.gentoo.org/ --with-pkgversion='Gentoo 12.1.1_p20220625 p8' --disable-esp --enable-libstdcxx-time --disable-libstdcxx-pch --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-multilib --with-multilib-list=m32,m64 --disable-fixed-point --enable-targets=all --enable-libgomp --disable-libssp --disable-libada --disable-cet --disable-systemtap --disable-valgrind-annotations --disable-vtable-verify --disable-libvtv --without-zstd --enable-lto --with-isl --disable-isl-version-check --enable-default-pie --enable-default-ssp --with-build-config=bootstrap-lto
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 12.1.1 20220625 (Gentoo 12.1.1_p20220625 p8) 
C compiler:
Attempting to autodetect OpenMP support... Compiler supports OpenMP
Attempting to autodetect SSE3   support... Compiler supports SSE3
Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
Attempting to autodetect NEON   support... Did not detect NEON support

Compiling mdtraj/formats/xtc/xtc.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/formats/xtc/trr.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/formats/tng/tng.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/formats/dcd/dcd.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/formats/binpos/binpos.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/formats/dtr/dtr.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/rmsd/_rmsd.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libc/string.pxd.
Compiling mdtraj/rmsd/_lprmsd.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd.
Compiling mdtraj/geometry/src/_geometry.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd.
Compiling mdtraj/geometry/neighbors.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd.
Compiling mdtraj/geometry/neighborlist.pyx because it depends on /usr/lib/python3.8/site-packages/Cython/Includes/libcpp/vector.pxd.
[ 1/11] Cythonizing mdtraj/formats/dcd/dcd.pyx
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[11/11] Cythonizing mdtraj/rmsd/_rmsd.pyx
running build
running build_py
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
copying mdtraj/version.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
copying mdtraj/io.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
copying mdtraj/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/zipped.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/validation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/unitcell.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/six.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/singleton.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/rotation.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/delay_import.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/contextmanagers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
copying mdtraj/utils/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/testing.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/docstrings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/docscrape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
copying mdtraj/testing/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/testing
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
copying mdtraj/scripts/mdinspect.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
copying mdtraj/scripts/mdconvert.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
copying mdtraj/scripts/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/scripts
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/xtcreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/netcdfreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/hdf5reporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/dcdreporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/basereporter.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
copying mdtraj/reporters/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/reporters
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
copying mdtraj/nmr/shift_wrappers.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
copying mdtraj/nmr/scalar_couplings.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
copying mdtraj/nmr/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/nmr
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/thermodynamic_properties.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/shape.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/sasa.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/rg.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/rdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/order.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/internal.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/hbond.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/dssp.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/distance.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/dihedral.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/contact.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/angle.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/alignment.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
copying mdtraj/geometry/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/xyzfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/registry.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/psf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/prmtop.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/openmmxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/netcdf.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/mol2.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/mdcrd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/lh5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/lammpstrj.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/hoomdxml.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/hdf5.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/gsd.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/gro.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/arc.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/amberrst.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
copying mdtraj/formats/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/trajectory.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/topology.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/selection.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/residue_names.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/element.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
copying mdtraj/core/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_operators.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_math.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit_definitions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/unit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/standard_dimensions.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/quantity.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/prefix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/mymatrix.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/doctests.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/constants.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/baseunit.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/basedimension.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
copying mdtraj/utils/unit/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/utils/unit
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbstructure.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/pdbfile.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
copying mdtraj/formats/pdb/__init__.py -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/residues.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data
copying mdtraj/formats/pdb/data/pdbNames.xml -> /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/pdb/data
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
building 'mdtraj.formats.xtc' extension
building 'mdtraj.formats.trr' extension
building 'mdtraj.formats.tng' extension
building 'mdtraj.formats.dcd' extension
building 'mdtraj.formats.binpos' extension
building 'mdtraj.formats.dtr' extension
building 'mdtraj._rmsd' extension
building 'mdtraj._lprmsd' extension
building 'mdtraj.core.lib.libtheobald' extension
building 'mdtraj.geometry._geometry' extension
building 'mdtraj.geometry.drid' extension
building 'mdtraj.geometry.neighbors' extension
building 'mdtraj.geometry.neighborlist' extension
INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src
INFO: C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -fPIC

creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src
INFO: compile options: '-Imdtraj/geometry/include -Imdtraj/geometry/src/kernels -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/_geometry.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/sasa.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/dssp.cpp
INFO: compile options: '-Imdtraj/geometry/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/geometry.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-msse2 -mssse3 -O3 -funroll-loops --std=c++11'
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/neighborlist.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc
INFO: compile options: '-Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/drid.cpp
INFO: compile options: '-Imdtraj/rmsd -Imdtraj/rmsd/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-fopenmp -msse2 -mssse3 -O3 -funroll-loops --std=c++11 -Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/neighbors.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: compile options: '-Imdtraj/formats/dcd/include/ -Imdtraj/formats/dcd/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/_rmsd.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/dridkernels.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/_lprmsd.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/neighbors.cpp
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/neighborlist.cpp
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/geometry/src/moments.cpp
INFO: compile options: '-Imdtraj/formats/binpos/include/ -Imdtraj/formats/binpos/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src
creating /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib
INFO: compile options: '-DDESRES_READ_TIMESTEP2=1 -Imdtraj/formats/dtr/include/ -Imdtraj/formats/dtr/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: compile options: '-Imdtraj/formats/xtc/include/ -Imdtraj/formats/xtc/ -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
extra options: '-Wno-unused-function -Wno-unreachable-code -Wno-sign-compare'
INFO: compile options: '-DUSE_ZLIB=1 -Imdtraj/formats/tng/include -I/usr/include -I/usr/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c'
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/fancy_index.cpp
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/geometry/src/_geometry.cpp:810:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/dcd/dcd.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/Munkres.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/euclidean_permutation.cpp
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/rmsd/_lprmsd.cpp:808:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dcd/dcd.c:776:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/dcd/src/dcdplugin.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/trr.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: x86_64-pc-linux-gnu-ar: adding 2 object files to /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/core/lib/libtheobald.a
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_trr.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/binpos/binpos.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/binpos/src/binposplugin.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/dtr/dtr.cpp
mdtraj/formats/binpos/src/binposplugin.c: In function ‘open_binpos_read’:
mdtraj/formats/binpos/src/binposplugin.c:59:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   59 |   fread(magicchar,sizeof(char),4,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdtraj/formats/binpos/src/binposplugin.c:69:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   69 |   fread(&igarb,sizeof(int),1,fd);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/dtr/src/dtrplugin.cxx
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/trr.c:778:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/xtc.c
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/dtr/dtr.cpp:797:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/binpos/binpos.c:776:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/tng.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc3.c
INFO: x86_64-pc-linux-gnu-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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/dcd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dcd/src/dcdplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dcd.cpython-38-x86_64-linux-gnu.so
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/xtc/xtc.c:778:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
In file included from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from mdtraj/formats/tng/tng.c:804:
/usr/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
lto-wrapper: warning: using serial compilation of 2 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile_xtc.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/xtc2.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/widemuldiv.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/warnmalloc.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/vals16.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/tng_compress.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/rle.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/mtf.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/merge_sort.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/lz77.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffmem.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/huffman.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/fixpoint.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/dict.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/coder.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/rotation.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
INFO: x86_64-pc-linux-gnu-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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/binpos.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/binpos/src/binposplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/binpos.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/src/xdr_seek.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/xtc/src/xdrfile.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwt.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/compression/bwlzh.c
lto-wrapper: warning: using serial compilation of 2 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/lib/tng_io.c
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/formats/tng/src/lib/md5.c
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/drid.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/dridkernels.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/moments.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/drid.cpython-38-x86_64-linux-gnu.so
mdtraj/formats/dtr/src/dtrplugin.cxx: In member function ‘bool desres::molfile::Timekeys::init(const std::string&)’:
mdtraj/formats/dtr/src/dtrplugin.cxx:487:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
  487 |             printf("size %d framesize %d\n\n",
      |                          ~^
      |                           |
      |                           int
      |                          %ld
  488 |                     keys[i].size(), m_framesize);
      |                     ~~~~~~~~~~~~~~
      |                                 |
      |                                 uint64_t {aka long unsigned int}
mdtraj/formats/dtr/src/dtrplugin.cxx:487:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
  487 |             printf("size %d framesize %d\n\n",
      |                                       ~^
      |                                        |
      |                                        int
      |                                       %ld
  488 |                     keys[i].size(), m_framesize);
      |                                     ~~~~~~~~~~~
      |                                     |
      |                                     uint64_t {aka long unsigned int}
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_block_header_read’:
mdtraj/formats/tng/src/lib/tng_io.c:1064:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)’} [-Wincompatible-pointer-types]
 1064 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1073:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)’} [-Wincompatible-pointer-types]
 1073 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1089:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)’} [-Wincompatible-pointer-types]
 1089 |                 tng_data->input_endianness_swap_func_32 =
      |                                                         ^
mdtraj/formats/tng/src/lib/tng_io.c:1098:57: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)’} [-Wincompatible-pointer-types]
 1098 |                 tng_data->input_endianness_swap_func_64 =
      |                                                         ^
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/neighborlist.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighborlist.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighborlist.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/center.cpp
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_get’:
mdtraj/formats/tng/src/lib/tng_io.c:9565:53: warning: comparison of distinct pointer types lacks a cast
 9565 |         if(tng_data->output_endianness_swap_func_32 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9570:58: warning: comparison of distinct pointer types lacks a cast
 9570 |         else if(tng_data->output_endianness_swap_func_32 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c:9588:53: warning: comparison of distinct pointer types lacks a cast
 9588 |         if(tng_data->output_endianness_swap_func_64 ==
      |                                                     ^~
mdtraj/formats/tng/src/lib/tng_io.c:9593:58: warning: comparison of distinct pointer types lacks a cast
 9593 |         else if(tng_data->output_endianness_swap_func_64 ==
      |                                                          ^~
mdtraj/formats/tng/src/lib/tng_io.c: In function ‘tng_output_file_endianness_set’:
mdtraj/formats/tng/src/lib/tng_io.c:9651:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)’} [-Wincompatible-pointer-types]
 9651 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9660:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)’} [-Wincompatible-pointer-types]
 9660 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9673:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint32_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  unsigned int *)’} [-Wincompatible-pointer-types]
 9673 |             tng_data->output_endianness_swap_func_32 =
      |                                                      ^
mdtraj/formats/tng/src/lib/tng_io.c:9682:54: warning: assignment to ‘tng_function_status (*)(struct tng_trajectory * const,  int64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long int *)’} from incompatible pointer type ‘tng_function_status (*)(struct tng_trajectory * const,  uint64_t *)’ {aka ‘tng_function_status (*)(struct tng_trajectory * const,  long unsigned int *)’} [-Wincompatible-pointer-types]
 9682 |             tng_data->output_endianness_swap_func_64 =
      |                                                      ^
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/neighbors.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/neighbors.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/neighbors.cpython-38-x86_64-linux-gnu.so
lto-wrapper: warning: using serial compilation of 3 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
lto-wrapper: warning: using serial compilation of 3 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-gcc: mdtraj/rmsd/src/theobald_rmsd.cpp
lto-wrapper: warning: using serial compilation of 3 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_trr.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so
mdtraj/formats/xtc/include/trr_header.h:28:5: error: type of ‘do_trnheader’ does not match original declaration [-Werror=lto-type-mismatch]
   28 | int do_trnheader(XDRFILE *xd, char bRead, t_trnheader *sh);
      |     ^
mdtraj/formats/xtc/src/xdrfile_trr.c:90:12: note: type mismatch in parameter 2
   90 | extern int do_trnheader(XDRFILE *xd,mybool bRead,t_trnheader *sh)
      |            ^
mdtraj/formats/xtc/src/xdrfile_trr.c:90:12: note: type ‘mybool’ should match type ‘char’
mdtraj/formats/xtc/src/xdrfile_trr.c:90:12: note: ‘do_trnheader’ was previously declared here
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/_lprmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/fancy_index.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/Munkres.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/euclidean_permutation.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_lprmsd.cpython-38-x86_64-linux-gnu.so
lto1: some warnings being treated as errors
lto-wrapper: fatal error: x86_64-pc-linux-gnu-gcc returned 1 exit status
compilation terminated.
/usr/lib/gcc/x86_64-pc-linux-gnu/12.1.1/../../../../x86_64-pc-linux-gnu/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/_geometry.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/sasa.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/dssp.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/geometry/src/geometry.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/geometry/_geometry.cpython-38-x86_64-linux-gnu.so
lto-wrapper: warning: using serial compilation of 3 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/xtc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_xtc.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/xtc.cpython-38-x86_64-linux-gnu.so
lto-wrapper: warning: using serial compilation of 5 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
lto-wrapper: warning: using serial compilation of 3 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/theobald_rmsd.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/rotation.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/rmsd/src/center.o -L/usr/lib64 -lgomp -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/_rmsd.cpython-38-x86_64-linux-gnu.so
INFO: x86_64-pc-linux-gnu-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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/tng.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc3.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/xtc2.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/widemuldiv.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/warnmalloc.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/vals16.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/tng_compress.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/rle.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/mtf.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/merge_sort.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/lz77.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffmem.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/huffman.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/fixpoint.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/dict.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/coder.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwt.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/compression/bwlzh.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/tng_io.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/tng/src/lib/md5.o -L/usr/lib -L/usr/lib64 -lz -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/tng.cpython-38-x86_64-linux-gnu.so
/usr/lib/gcc/x86_64-pc-linux-gnu/12.1.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/12.1.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc
lto-wrapper: warning: using serial compilation of 5 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
lto-wrapper: warning: using serial compilation of 8 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
INFO: x86_64-pc-linux-gnu-g++ -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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/dtr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/dtr/src/dtrplugin.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/dtr.cpython-38-x86_64-linux-gnu.so
lto-wrapper: warning: using serial compilation of 3 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
error: Command "x86_64-pc-linux-gnu-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 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/trr.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdr_seek.o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/temp.linux-x86_64-3.8/mdtraj/formats/xtc/src/xdrfile_trr.o -L/usr/lib64 -o /var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7-python3_8/lib/mdtraj/formats/trr.cpython-38-x86_64-linux-gnu.so" failed with exit status 1
 * ERROR: sci-chemistry/mdtraj-1.9.7::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  122:  Called src_compile
 *   environment, line 3432:  Called distutils-r1_src_compile
 *   environment, line 1623:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
 *   environment, line  762:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 3119:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2648:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2646:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 1089:  Called distutils-r1_run_phase 'distutils-r1_python_compile'
 *   environment, line 1605:  Called distutils-r1_python_compile
 *   environment, line 1407:  Called esetup.py 'build' '-j' '16'
 *   environment, line 2187:  Called die
 * The specific snippet of code:
 *       "${@}" || die -n;
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/mdtraj-1.9.7::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/mdtraj-1.9.7::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/mdtraj-1.9.7:20220730-180712.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7'
 * S: '/var/tmp/portage/sci-chemistry/mdtraj-1.9.7/work/mdtraj-1.9.7'