build.log

build.log (text/plain), 10.86 KB, created by Agostino Sarubbo on 2020-06-11 16:19:33 UTC

 * Package:    sci-chemistry/modeller-9.22
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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