* Package: sci-chemistry/modeller-9.22 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 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/0e625ca98e45876eb61e2934be6fbe8d923e4447 @@@@@ END @@@@@ >>> Unpacking source... >>> Unpacking modeller-9.22.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.22/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.22/work >>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22 ... * python2_7: running distutils-r1_run_phase python_compile * DISTUTILS_USE_SETUPTOOLS value is probably incorrect * value: DISTUTILS_USE_SETUPTOOLS=bdepend (default?) * expected: DISTUTILS_USE_SETUPTOOLS=no python2.7 setup.py build running build running build_ext building '_modeller' extension creating /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22-python2_7/temp.linux-x86_64-2.7 x86_64-pc-linux-gnu-gcc -fno-strict-aliasing -O2 -pipe -march=native -frecord-gcc-switches -fwrapv -DNDEBUG -O2 -pipe -march=native -frecord-gcc-switches -fcommon -fPIC -I../include -I../include/x86_64-intel8 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/python2.7 -c modeller_wrap.c -o /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22-python2_7/temp.linux-x86_64-2.7/modeller_wrap.o In file included from /usr/include/string.h:495, from /usr/include/python2.7/Python.h:38, from modeller_wrap.c:154: In function ‘memcpy’, inlined from ‘python_to_f_str_array’ at modeller_wrap.c:2996:7: /usr/include/bits/string_fortified.h:34:10: warning: ‘__builtin_memcpy’ writing one too many bytes into a region of a size that depends on ‘strlen’ [-Wstringop-overflow=] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modeller_wrap.c: In function ‘python_to_f_str_array’: modeller_wrap.c:2995:16: note: at offset 0 to an object with size between 1 and 18446744073709551615 allocated by ‘malloc’ here 2995 | result = malloc(len); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=native -frecord-gcc-switches -fcommon /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22-python2_7/temp.linux-x86_64-2.7/modeller_wrap.o -L../../lib/x86_64-intel8 -L/usr/lib64 -lmodeller -lglib-2.0 -lpython2.7 -o /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22-python2_7/lib/_modeller.so >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/modeller-9.22 >>> Install sci-chemistry/modeller-9.22 into /var/tmp/portage/sci-chemistry/modeller-9.22/image * python2_7: running distutils-r1_run_phase python_install python2.7 setup.py install --skip-build --root=/var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7 running install running install_lib creating /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7 creating /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7/usr creating /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7/usr/lib64 creating /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7/usr/lib64/python2.7 creating /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7/usr/lib64/python2.7/site-packages copying /var/tmp/portage/sci-chemistry/modeller-9.22/work/modeller-9.22-python2_7/lib/_modeller.so -> /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7/usr/lib64/python2.7/site-packages running install_egg_info Writing /var/tmp/portage/sci-chemistry/modeller-9.22/image/_python2.7/usr/lib64/python2.7/site-packages/Modeller-0.0.0-py2.7.egg-info * Using python2.7 in global scope * python2_7: running distutils-r1_run_phase python_install_all * python2_7: running python_domodule modlib/modeller * python2_7: running python_doscript bin/modslave.py >>> Completed installing sci-chemistry/modeller-9.22 into /var/tmp/portage/sci-chemistry/modeller-9.22/image * Final size of build directory: 118836 KiB (116.0 MiB) * Final size of installed tree: 57688 KiB ( 56.3 MiB) * Verifying compiled files in /usr/lib64/python2.7/site-packages strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/lib64/python2.7/site-packages/_modeller.so /opt/modeller/lib/x86_64-intel8/libintlc.so.5 /opt/modeller/lib/x86_64-intel8/libifcore.so.5 /opt/modeller/lib/x86_64-intel8/libimf.so /opt/modeller/lib/x86_64-intel8/libsaxs.so /opt/modeller/lib/x86_64-intel8/libsvml.so >>> Done. * QA Notice: Symbolic link /usr/lib64/libmodeller.so.8 points to /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 which does not exist. * QA Notice: Symbolic link /opt/modeller/lib/x86_64-intel8/libmodeller.so points to /opt/modeller/lib/x86_64-intel8/libmodeller.so.8 which does not exist. * Obtain a license Key from * http://salilab.org/modeller/registration.html * And run this before using modeller: * emerge --config =sci-chemistry/modeller-9.22 * That way you can [re]enter your license key. emerge --info: Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r5, 5.4.0-1011-aws x86_64) ================================================================= System uname: Linux-5.4.0-1011-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 KiB Mem: 16011348 total, 976896 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 11 Jun 2020 14:35:16 +0000 sh bash 5.0_p17 ld GNU ld (Gentoo 2.34 p4) 2.34.0 app-shells/bash: 5.0_p17::gentoo dev-lang/perl: 5.30.3-r1::gentoo dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.20::gentoo sys-devel/autoconf: 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.34-r1::gentoo sys-devel/gcc: 10.1.0::gentoo sys-devel/gcc-config: 2.3::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r5::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-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fcommon" 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/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fcommon" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" ENV_UNSET="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=native -frecord-gcc-switches -fcommon" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect 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=native -frecord-gcc-switches -fcommon" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j4" PKGDIR="/root/.packages" 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" USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS