export LDFLAGS="-Wl,-O0 -Wl,--as-needed" export CFLAGS="-ggdb -pipe -march=sandybridge -mtune=native -ftree-vectorize" export CXXFLAGS="-ggdb -pipe -march=sandybridge -mtune=native -ftree-vectorize" FEATURES=noclean emerge glibc dev-python/wxpython dev-lang/python:2.7 emerge -uN biopython >>> Emerging (1 of 2) dev-python/matplotlib-2.1.2-r1::gentoo * matplotlib-2.1.2.tar.bz2 BLAKE2B SHA512 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking matplotlib-2.1.2.tar.bz2 to /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work >>> Source unpacked in /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work >>> Preparing source in /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2 ... * Applying matplotlib-2.1.2-doc-make.patch ... [ ok ] * Will copy sources from /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2 * python2_7: copying to /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2-python2_7 * python3_4: copying to /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2-python3_4 * python3_5: copying to /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2-python3_5 >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2 ... * python2_7: running distutils-r1_run_phase python_configure * python3_4: running distutils-r1_run_phase python_configure * python3_5: running distutils-r1_run_phase python_configure * python3_5: running distutils-r1_run_phase python_configure_all >>> Source configured. >>> Compiling source in /scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2 ... * python2_7: running distutils-r1_run_phase python_compile /usr/bin/python2.7 setup.py build --build-lib=/scratch/var/tmp/portage/dev-python/matplotlib-2.1.2-r1/work/matplotlib-2.1.2-python2_7/build/lib ============================================================================ Edit setup.cfg to change the build options BUILDING MATPLOTLIB matplotlib: yes [2.1.2-python2_7] python: yes [2.7.14 (default, Feb 3 2018, 10:18:21) [GCC 6.4.0]] platform: yes [linux2] REQUIRED DEPENDENCIES AND EXTENSIONS numpy: yes [version 1.13.3] six: yes [using six version 1.11.0] dateutil: yes [using dateutil version 2.6.1] backports.functools_lru_cache: yes [using backports.functools_lru_cache] subprocess32: yes [using subprocess32] pytz: yes [using pytz version 2017.2] cycler: yes [using cycler version 0.10.0] tornado: yes [using tornado version 4.5.1] pyparsing: yes [using pyparsing version 2.2.0] libagg: yes [pkg-config information for 'libagg' could not be found. Using local copy.] freetype: yes [version 2.9.0] png: yes [version 1.6.34] qhull: yes [Using system Qhull (version unknown, no pkg- config info)] OPTIONAL SUBPACKAGES sample_data: yes [installing] toolkits: yes [installing] tests: no [skipping due to configuration] toolkits_tests: no [skipping due to configuration] OPTIONAL BACKEND EXTENSIONS macosx: no [Mac OS-X only] qt5agg: yes [installing, Qt: 5.9.2, PyQt: 5.9.2; PySide2 not found] qt4agg: no [skipping due to configuration] gtk3agg: yes [installing, version 3.26.22] *** Error in `/usr/bin/python2.7': double free or corruption (out): 0x00007ffd3128c550 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x77beb)[0x7fec52eb0beb] /lib64/libc.so.6(+0x7f84e)[0x7fec52eb884e] /lib64/libc.so.6(+0x8012e)[0x7fec52eb912e] /usr/lib64/python2.7/site-packages/wx-3.0-gtk2/wx/_core_.so(_ZN8wxString15ConvertedBufferIcED2Ev+0x1b)[0x7fec39ba6439] /usr/lib64/python2.7/site-packages/wx-3.0-gtk2/wx/_core_.so(_ZN8wxStringD2Ev+0x1c)[0x7fec39ba223a] /usr/lib64/libwx_baseu-3.0.so.0(+0xdf120)[0x7fec387c3120] /usr/lib64/libwx_baseu-3.0.so.0(+0x1428f2)[0x7fec388268f2] /usr/lib64/libwx_baseu-3.0.so.0(_ZNK8wxCSConv8DoCreateEv+0x7c4)[0x7fec3882af14] /usr/lib64/libwx_baseu-3.0.so.0(_ZN8wxCSConvC2E14wxFontEncoding+0x88)[0x7fec3882d1b8] /usr/lib64/libwx_baseu-3.0.so.0(_Z20wxGet_wxConvLocalPtrv+0x49)[0x7fec3882d229] /usr/lib64/libwx_baseu-3.0.so.0(+0x6b6ae)[0x7fec3874f6ae] /lib64/ld-linux-x86-64.so.2(+0xf52a)[0x7fec53a8652a] /lib64/ld-linux-x86-64.so.2(+0xf63b)[0x7fec53a8663b] /lib64/ld-linux-x86-64.so.2(+0x13b88)[0x7fec53a8ab88] /lib64/libc.so.6(_dl_catch_error+0x84)[0x7fec52f729a4] /lib64/ld-linux-x86-64.so.2(+0x13329)[0x7fec53a8a329] /lib64/libdl.so.2(+0x10fe)[0x7fec52c360fe] /lib64/libc.so.6(_dl_catch_error+0x84)[0x7fec52f729a4] /lib64/libdl.so.2(+0x18f1)[0x7fec52c368f1] /lib64/libdl.so.2(dlopen+0x42)[0x7fec52c361a2] /usr/lib64/libpython2.7.so.1.0(_PyImport_GetDynLoadFunc+0x279)[0x7fec53580fd6] /usr/lib64/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0xa7)[0x7fec5355e45a] /usr/lib64/libpython2.7.so.1.0(+0x149bcd)[0x7fec5355abcd] /usr/lib64/libpython2.7.so.1.0(+0x14b8c6)[0x7fec5355c8c6] /usr/lib64/libpython2.7.so.1.0(+0x14b08a)[0x7fec5355c08a] /usr/lib64/libpython2.7.so.1.0(+0x14a47d)[0x7fec5355b47d] /usr/lib64/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x3f)[0x7fec5355b830] /usr/lib64/libpython2.7.so.1.0(+0x11aec6)[0x7fec5352bec6] /usr/lib64/libpython2.7.so.1.0(PyCFunction_Call+0xbc)[0x7fec534b31f6] /usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x84)[0x7fec53460a00] /usr/lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x112)[0x7fec5353ef20] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x61ff)[0x7fec53539fbd] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0xef5)[0x7fec5353d7c8] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x41)[0x7fec53533d99] /usr/lib64/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x143)[0x7fec535587bb] /usr/lib64/libpython2.7.so.1.0(+0x148338)[0x7fec53559338] /usr/lib64/libpython2.7.so.1.0(+0x149b8d)[0x7fec5355ab8d] /usr/lib64/libpython2.7.so.1.0(+0x14b8c6)[0x7fec5355c8c6] /usr/lib64/libpython2.7.so.1.0(+0x14b08a)[0x7fec5355c08a] /usr/lib64/libpython2.7.so.1.0(+0x14a4fd)[0x7fec5355b4fd] /usr/lib64/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x3f)[0x7fec5355b830] /usr/lib64/libpython2.7.so.1.0(+0x11aec6)[0x7fec5352bec6] /usr/lib64/libpython2.7.so.1.0(PyCFunction_Call+0xbc)[0x7fec534b31f6] /usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x84)[0x7fec53460a00] /usr/lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x112)[0x7fec5353ef20] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x61ff)[0x7fec53539fbd] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0xef5)[0x7fec5353d7c8] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCode+0x41)[0x7fec53533d99] /usr/lib64/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x143)[0x7fec535587bb] /usr/lib64/libpython2.7.so.1.0(+0x148338)[0x7fec53559338] /usr/lib64/libpython2.7.so.1.0(+0x149b8d)[0x7fec5355ab8d] /usr/lib64/libpython2.7.so.1.0(+0x1485f7)[0x7fec535595f7] /usr/lib64/libpython2.7.so.1.0(+0x149be9)[0x7fec5355abe9] /usr/lib64/libpython2.7.so.1.0(+0x14b8c6)[0x7fec5355c8c6] /usr/lib64/libpython2.7.so.1.0(+0x14b08a)[0x7fec5355c08a] /usr/lib64/libpython2.7.so.1.0(+0x14a47d)[0x7fec5355b47d] /usr/lib64/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x3f)[0x7fec5355b830] /usr/lib64/libpython2.7.so.1.0(+0x11aec6)[0x7fec5352bec6] /usr/lib64/libpython2.7.so.1.0(PyCFunction_Call+0xbc)[0x7fec534b31f6] /usr/lib64/libpython2.7.so.1.0(PyObject_Call+0x84)[0x7fec53460a00] /usr/lib64/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x112)[0x7fec5353ef20] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x61ff)[0x7fec53539fbd] /usr/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0xef5)[0x7fec5353d7c8] ======= Memory map: ======== ...
Created attachment 517638 [details] build.log
Thank you for the report. Please provide the emerge --info https://wiki.gentoo.org/wiki/Attach_the_logs_to_the_bug_ticket and reopen this ticket (Status:unconfirmed).
# emerge --info dev-python/matplotlib Portage 2.3.22 (python 2.7.14-final-0, default/linux/amd64/17.0, gcc-6.4.0, glibc-2.25-r10, 4.14.15 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.14.15-x86_64-Intel-R-_Core-TM-_i7-7820HQ_CPU_@_2.90GHz-with-gentoo-2.4.1 KiB Mem: 8098440 total, 864732 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Fri, 02 Feb 2018 22:00:01 +0000 Head commit of repository gentoo: f0cb40339b06568a41830351156e12c5c6bacb3d sh bash 4.4_p18 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.4_p18::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.9999::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.4.6-r1::gentoo, 3.5.4-r1::gentoo, 3.6.4::gentoo dev-util/cmake: 3.10.2::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.34.11::gentoo sys-apps/sandbox: 2.12::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15.1-r1::gentoo sys-devel/binutils: 2.25.1-r1::gentoo, 2.27::gentoo, 2.28-r2::gentoo, 2.29.1-r1::gentoo, 2.30::gentoo sys-devel/gcc: 4.2.4-r1::gentoo, 4.3.6-r1::gentoo, 4.4.7::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.4::gentoo, 5.4.0-r3::gentoo, 6.3.0::gentoo, 6.4.0::gentoo, 7.2.0-r1::gentoo, 7.3.0::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r1::gentoo sys-kernel/linux-headers: 4.15::gentoo (virtual/os-headers) sys-libs/glibc: 2.25-r10::gentoo Repositories: gentoo location: /scratch/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: x-portage location: /scratch/usr/local/portage masters: gentoo priority: 0 x-layman location: /scratch/var/lib/layman masters: gentoo priority: 1 haskell location: /var/lib/layman/haskell masters: gentoo priority: 50 science location: /var/lib/layman/science masters: gentoo priority: 50 vmware location: /var/lib/layman/vmware masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x OPERA-2014 RAR" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=sandybridge -mtune=native -ftree-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -march=sandybridge -mtune=native -ftree-vectorize" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en_US en_GB en cs" MAKEOPTS="-j5" PKGDIR="/usr/portage/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="/scratch/var/tmp" USE="X acpi alsa amd64 amr apache apache2 asm avx avx2 berkdb bindist bluetooth boost bzip2 cairo cgi cli coin consolekit cracklib crypt cryptlib cryptsetup cups cxx dbus device-mapper dhcp directfb drm dvd emboss encode fax fbcon ffmpeg flac fontconfig fortran gbm gcrypt gd gdbm geoip gimp glpk gmp gnutls gpm gps gtk hal hpijs hwdb iconv id3tag imaging innodb inotify java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack laptop lcms libnotify lm_sensors mad matroska mmx modemmanager modules multilib ncurses nfs nls nptl nptlonly nscd nss ntfsprogs objc ocr ogg opengl openmp openssl pam parport pcre pcre16 pdf perl php png policykit polkit ppds pppd python qt3support qt4 qt5 readline rendering resolvconf romio scanner sctp seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification suexec svg syslog tcl tcpd threads tiff tk truetype udev unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xattr xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64 32" 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="alias authz_host auth_basic auth_digest cgi cgid deflate dir env filter include info mem_cache mime mime_magic negotiation remoteip setenvif status userdir vhost_alias rewrite usertrack cache file_cache disk_cache charset_lite log_config log_forensic" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 navcom ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tnt tripmate tsip ublox fury geostar nmea0183 nmea2000 passthrough" GRUB_PLATFORMS="pc efi-64" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en-US en en-GB cs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4 python3_5" RUBY_TARGETS="ruby21 ruby23 ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 i965" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-python/matplotlib-2.1.2-r1::gentoo was built with the following: USE="cairo gtk3 qt5 tk wxwidgets -doc -examples -excel -gtk2 -latex -pyside -test" ABI_X86="(64)" PYTHON_TARGETS="python2_7 python3_4 python3_5 -python3_6" CFLAGS="-O2 -pipe -march=sandybridge -mtune=native -ftree-vectorize -fno-strict-aliasing" CXXFLAGS="-O2 -pipe -march=sandybridge -mtune=native -ftree-vectorize -fno-strict-aliasing"
Not great, but this is from a while ago. If it's still happening, please come back with debugging symbols as per https://wiki.gentoo.org/wiki/Debugging?
