Created attachment 598042 [details] full build log /usr/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_so_flags = self.flag_vars.linker_so /usr/lib/python3.7/site-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_exe_flags = self.flag_vars.linker_exe error: Command "/usr/bin/gfortran -Wall -g -Wl,-O1 -Wl,--as-needed -shared /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/src.linux-x86_64-3.7/scipy/integrate/lsodamodule.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/src.linux-x86_64-3.7/scipy/integrate/fortranobject.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0 -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7 -llsoda -lmach -llapack -lblas -lcblas -lpython3.7m -lgfortran -o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/lib/scipy/integrate/lsoda.cpython-37m-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/link-version-scipy.integrate.lsoda.map" failed with exit status 1 [31;01m*[0m ERROR: sci-libs/scipy-1.1.0::gentoo failed (compile phase): [31;01m*[0m (no error message) [31;01m*[0m [31;01m*[0m Call stack: [31;01m*[0m ebuild.sh, line 125: Called src_compile [31;01m*[0m environment, line 4281: Called distutils-r1_src_compile [31;01m*[0m environment, line 1249: Called _distutils-r1_run_foreach_impl 'python_compile' [31;01m*[0m environment, line 407: Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile' [31;01m*[0m environment, line 3713: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' [31;01m*[0m environment, line 2870: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' [31;01m*[0m environment, line 2868: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' [31;01m*[0m environment, line 872: Called distutils-r1_run_phase 'python_compile' [31;01m*[0m environment, line 1242: Called python_compile [31;01m*[0m environment, line 3318: Called distutils-r1_python_compile 'config_fc' '--noopt' '--noarch' [31;01m*[0m environment, line 1110: Called esetup.py 'build' '-j' '5' 'config_fc' '--noopt' '--noarch' [31;01m*[0m environment, line 1898: Called die [31;01m*[0m The specific snippet of code: [31;01m*[0m "${@}" || die "${die_args[@]}"; [31;01m*[0m [31;01m*[0m If you need support, post the output of `emerge --info '=sci-libs/scipy-1.1.0::gentoo'`, [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-libs/scipy-1.1.0::gentoo'`. [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-libs/scipy-1.1.0/temp/build.log'. [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-1.1.0/temp/environment'. [31;01m*[0m Working directory: '/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7' [31;01m*[0m S: '/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0'
Created attachment 598044 [details] emerge --info output
same problem here -
I'm also affected by this issue. (GCC 9.2.0 hardened)
I'm seeing the same thing with scipy-1.4.1.
same here, scipy-1.4.1 with gcc-9.2 error: Command "/usr/bin/gfortran -Wall -g -Wl,--as-needed -Wl,--hash-style=gnu -shared /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/src.linux-x86_64-3.7/scipy/linalg/_flinalgmodule.o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/src.linux-x86_64-3.7/scipy/linalg/fortranobject.o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/temp.linux-x86_64-3.7/scipy/linalg/src/det.o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/temp.linux-x86_64-3.7/scipy/linalg/src/lu.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0 -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/temp.linux-x86_64-3.7 -llapack -lblas -lcblas -lpython3.7m -lgfortran -o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/lib/scipy/linalg/_flinalg.cpython-37m-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_7/build/temp.linux-x86_64-3.7/link-version-scipy.linalg._flinalg.map" failed with exit status 1 * ERROR: sci-libs/scipy-1.4.1::gentoo failed (compile phase): Portage 2.3.84 (python 3.7.6-final-0, default/linux/amd64/17.1/desktop, gcc-9.2.0, glibc-2.30-r3, 5.4.4-gentoo x86_64) ================================================================= System uname: Linux-5.4.4-gentoo-x86_64-AMD_Ryzen_5_1600_Six-Core_Processor-with-gentoo-2.6 KiB Mem: 32900436 total, 22030964 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sun, 29 Dec 2019 01:05:52 +0000 Head commit of repository gentoo: c33e5ce8833c24ea79aad297f41697921acb606b sh bash 5.0_p11 ld GNU gold (Gentoo 2.33.1 p1 2.33.1) 1.16 app-shells/bash: 5.0_p11::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.30.1::gentoo dev-lang/python: 2.7.17::gentoo, 3.6.10::gentoo, 3.7.6::gentoo, 3.8.1::gentoo dev-util/cmake: 3.16.2-r1::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.1-r2::gentoo sys-devel/binutils: 2.33.1::gentoo sys-devel/gcc: 6.4.0-r5::gentoo, 9.2.0-r3::gentoo sys-devel/gcc-config: 2.1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 5.4::gentoo (virtual/os-headers) sys-libs/glibc: 2.30-r3::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: https://anongit.gentoo.org/git/repo/sync/gentoo.git priority: -1000 sync-git-verify-commit-signature: true ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -fomit-frame-pointer -march=native -fno-lto -mindirect-branch=thunk -ftree-vectorize -ftree-slp-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" 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" CXXFLAGS="-O2 -pipe -fomit-frame-pointer -march=native -fno-lto -mindirect-branch=thunk -ftree-vectorize -ftree-slp-vectorize" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--jobs 3" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync metadata-transfer multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.bytemark.co.uk/gentoo/ http://www.mirrorservice.org/sites/distfiles.gentoo.org/" LANG="en_GB.utf8" LDFLAGS="-Wl,--as-needed -Wl,--hash-style=gnu" LINGUAS="en en_GB uk" MAKEOPTS="-j6" PKGDIR="/var/cache/binpkgs" 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="X a52 aac acl acpi aiglx alsa amd64 bash-completion berkdb binddist branding bzip2 cairo cblas-external cdda cdr cleartype cli consolekit corefonts crypt cups cxx dri dts dvd dvdr emboss encode eselect-ldso evdev exif fam ffmpeg flac fortran gcc64 gdbm gegl gif gpm graphite gstreamer gtk iconv icu imlib introspection ipv6 java jpeg lcms libnotify libtirpc lto mad mng mp3 mp4 mpeg multilib ncurses nls nptl nptlonly nsplugin ogg opengl openmp oss pam pango pcre pdf pgo png policykit ppds pulseaudio python qt4 qt5 readline samba sdl seccomp smbclient spell split-usr ssl startup-notification svg tcpd threads tiff truetype type1 udev udisks unicode upower usb vorbis webkit wxwidgets x264 xattr xcb xml xulrunner xv xvid zlib" ABI_X86="64 32" 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="f16c mmx mmxext popcnt sse sse2 sse3 sse4a ssse" CURL_SSL="gnutls" 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" GRUB_PLATFORMS="efi-64 efi-32" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="en en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python3_6 python3_7 python3_8" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="nvidia vesa" 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, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
emerge changed to disable py37 (ie just py36, py38) sci-libs/scipy-1.4.1::gentoo USE="-doc -sparse -test" PYTHON_TARGETS="python3_6 python3_8 -python3_5 -python3_7" FAILS error: Command "/usr/bin/gfortran -Wall -g -Wl,--as-needed -Wl,--hash-style=gnu -shared /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/temp.linux-x86_64-3.8/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/src.linux-x86_64-3.8/scipy/linalg/_flinalgmodule.o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/temp.linux-x86_64-3.8/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/src.linux-x86_64-3.8/scipy/linalg/fortranobject.o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/temp.linux-x86_64-3.8/scipy/linalg/src/det.o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/temp.linux-x86_64-3.8/scipy/linalg/src/lu.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0 -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/temp.linux-x86_64-3.8 -llapack -lblas -lcblas -lgfortran -o /var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/lib/scipy/linalg/_flinalg.cpython-38-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.4.1/work/scipy-1.4.1-python3_8/build/temp.linux-x86_64-3.8/link-version-scipy.linalg._flinalg.map" failed with exit status 1 * ERROR: sci-libs/scipy-1.4.1::gentoo failed (compile phase):
sci-libs/scipy-1.4.1::gentoo USE="-doc -sparse -test" PYTHON_TARGETS="python3_6 -python3_5 -python3_7 -python3_8" 0 KiB >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-libs/scipy-1.4.1::gentoo >>> Jobs: 0 of 1 complete, 1 running Load avg: 2.26, 2.37, 2.04 >>> Installing (1 of 1) sci-libs/scipy-1.4.1::gentoo >>> Recording sci-libs/scipy in "world" favorites file... >>> Jobs: 1 of 1 complete Load avg: 1.40, 1.95, 1.93 py36 on its own works. Possibly something specific with py37, 38
scipy will build against py37 *IF* MAKEOPTS="-j1"
*** This bug has been marked as a duplicate of bug 614464 ***
(In reply to jon R-B from comment #8) > scipy will build against py37 *IF* MAKEOPTS="-j1" I can confirm that this allows scipy to be built (tested with scipy-1.1.0).
