hon3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/idzr_aid.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/idzr_asvd_subr_0.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/idzr_asvd_subr_1.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/idzr_rid.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/idzr_rsvd_subr_0.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/idzr_rsvd_subr_1.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/scipy/linalg/src/id_dist/src/prini.o -L/usr/lib64 -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6 -lblas -llapack -lblas -lcblas -lpython3.6m -lgfortran -o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/lib/scipy/linalg/_interpolative.cpython-36m-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/link-version-scipy.linalg._interpolative.map /usr/lib64/python3.6/site-packages/numpy/distutils/system_info.py:552: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. self.calc_info() Running from scipy source directory. /usr/lib64/python3.6/site-packages/numpy/distutils/system_info.py:644: UserWarning: Specified path /usr/lib64/python3.6/site-packages/numpy/__init__.py/include/python3.6m is invalid. return self.get_paths(self.section, key) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) 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_6/build/temp.linux-x86_64-3.6/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/src.linux-x86_64-3.6/src.linux-x86_64-3.6/scipy/linalg/_fblasmodule.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/src.linux-x86_64-3.6/src.linux-x86_64-3.6/scipy/linalg/fortranobject.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/scipy/_build_utils/src/wrap_dummy_g77_abi.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/scipy/_build_utils/src/wrap_dummy_accelerate.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/src.linux-x86_64-3.6/src.linux-x86_64-3.6/scipy/linalg/_fblas-f2pywrappers.o -L/usr/lib64 -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6 -lblas -llapack -lblas -lcblas -lpython3.6m -lgfortran -o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/lib/scipy/linalg/_fblas.cpython-36m-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_6/build/temp.linux-x86_64-3.6/link-version-scipy.linalg._fblas.map" failed with exit status 1 * ERROR: sci-libs/scipy-1.1.0::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 124: Called src_compile * environment, line 4166: Called distutils-r1_src_compile * environment, line 1205: Called _distutils-r1_run_foreach_impl 'python_compile' * environment, line 389: Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile' * environment, line 3599: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2737: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2735: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' * environment, line 855: Called distutils-r1_run_phase 'python_compile' * environment, line 1198: Called python_compile * environment, line 3185: Called distutils-r1_python_compile '-j' '8' 'config_fc' '--noopt' '--noarch' * environment, line 1073: Called esetup.py 'build' '-j' '8' 'config_fc' '--noopt' '--noarch' * environment, line 1758: Called die * The specific snippet of code: * "${@}" || die "${die_args[@]}"; Portage 2.3.40 (python 2.7.15-final-0, default/linux/amd64/17.0, gcc-7.3.0, glibc-2.27-r4, 4.17.1-gentoo x86_64) ================================================================= System uname: Linux-4.17.1-gentoo-x86_64-AMD_FX-tm-8350_Eight-Core_Processor-with-gentoo-2.6 KiB Mem: 16439336 total, 3190612 free KiB Swap: 0 total, 0 free sh bash 4.4_p23 ld GNU ld (Gentoo 2.30 p3) 2.30.0 app-shells/bash: 4.4_p23::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.15::gentoo, 3.5.5-r1::gentoo, 3.6.5-r1::gentoo dev-util/cmake: 3.11.4::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.6::gentoo sys-apps/openrc: 0.37::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.15.1-r2::gentoo, 1.16.1-r1::gentoo sys-devel/binutils: 2.30-r3::gentoo sys-devel/gcc: 7.3.0-r3::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r5::gentoo sys-devel/make: 4.2.1-r3::gentoo sys-kernel/linux-headers: 4.17::gentoo (virtual/os-headers) sys-libs/glibc: 2.27-r4::gentoo Repositories: gentoo location: /home/patrick/code/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: no sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 adjust location: /home/patrick/code/adjust/gentoo-overlay masters: gentoo priority: 0 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" 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 -march=native" DISTDIR="/chroot/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY 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-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch 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://distfiles.gentoo.org" INSTALL_MASK="/etc/X11/xinit/xinitrc.d/80-dbus /usr/bin/dbus-launch" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" 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="/var/tmp" USE="X acl alsa amd64 apng berkdb bzip2 cli crypt cups cxx dri ffmpeg fortran gdbm glamor gmp gpo iconv icu ipv6 lapack libtirpc minizip modules multilib ncurses nls nptl opencl opengl openmp pam pcre readline seccomp sqlite ssl tcpd udev unicode vdpau xattr 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="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 plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx f16c fma3 fma4 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3 xop" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" 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="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24" USERLAND="GNU" VIDEO_CARDS="radeon r600 radeonsi amdgpu" 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, LANG, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 536994 [details] gzipped build.log for current stable version, sci-libs/scipy-0.19.1 I'm also seeing this, with the current stable version, sci-libs/scipy-0.19.1. (I haven't tried 1.1.0 yet.) I'm attaching my build.log gzipped (it comes to over 1MB when uncompressed); my emerge --info is as follows: Portage 2.3.24 (python 2.7.14-final-0, default/linux/amd64/17.0, gcc-6.4.0, glibc-2.25-r11, 4.15.4-gentoo x86_64) ================================================================= System uname: Linux-4.15.4-gentoo-x86_64-Intel-R-_Core-TM-_i7-5820K_CPU_@_3.30GHz-with-gentoo-2.4.1 KiB Mem: 32916196 total, 11695916 free KiB Swap: 8191996 total, 8191996 free Timestamp of repository gentoo: Sat, 23 Jun 2018 00:45:01 +0000 sh bash 4.4_p12 ld GNU ld (Gentoo 2.29.1 p3) 2.29.1 ccache version 3.3.4 [disabled] app-shells/bash: 4.4_p12::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.24.3-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.4.8::gentoo, 3.5.5::gentoo, 3.6.5::gentoo dev-util/ccache: 3.3.4-r1::gentoo dev-util/cmake: 3.9.6::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: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.15.1-r2::gentoo sys-devel/binutils: 2.29.1-r1::gentoo sys-devel/gcc: 6.4.0-r1::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.25-r11::gentoo Repositories: gentoo location: /usr/portage sync-type: webrsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sph-local location: /opt/portage-overlay masters: gentoo priority: 0 abendbrot location: /var/lib/layman/abendbrot masters: gentoo priority: 50 anomen location: /var/lib/layman/anomen masters: gentoo priority: 50 gambas-overlay location: /var/lib/layman/gambas-overlay masters: gentoo priority: 50 lmiphay location: /var/lib/layman/lmiphay masters: gentoo priority: 50 netfab location: /var/lib/layman/netfab masters: gentoo priority: 50 palemoon location: /var/lib/layman/palemoon masters: gentoo priority: 50 stuff location: /var/lib/layman/stuff masters: gentoo priority: 50 x11 location: /var/lib/layman/x11 masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/avfs/extfs /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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--ask-enter-invalid --autounmask-keep-masks y" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync webrsync-gpg xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="https://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/" LANG="en_GB.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en en-GB" MAKEOPTS="-j13" 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="/var/tmp" USE="X a52 aac aacplus acl acpi alsa amd64 amr berkdb bluray bzip2 cairo cdda cddb cdio cdparanoia cli crypt cups cxx dbus dri dts dvd flac fluidsynth fontconfig fortran gdbm gpm gtk ibus iconv icu ipv6 jpeg libnotify libtirpc lzma mad mmx modplug modules mp3 mtp multilib ncurses nls nptl ogg opencl opengl openmp pam pcre png qt3support qt5 readline seccomp sound sse sse2 ssl startup-notification svg tcl tcpd theora tk truetype unicode v4l vdpau vim-syntax vorbis xattr xv xvmc zlib" ABI_X86="64" 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 plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 aes avx avx2 f16c fma3 pclmul popcnt sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" QEMU_SOFTMMU_TARGETS="x86_64 arm i386 mips mipsel ppc sparc" QEMU_USER_TARGETS="aarch64 alpha arm i386 m68k mips mipsel ppc sparc x86_64" RUBY_TARGETS="ruby23" USERLAND="GNU" VIDEO_CARDS="nouveau" 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_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Not just 1.1.0, also stable 0.19.1.
I suspect this is because numpy is not building with python 3.6, see bug 640928
Sorry, after further investigation that linked bug is not really relevant, I tried with numpy-1.13.3 and it's still not working.
Apparently this is a duplicate of Bug 614464 Building with MAKEOPTS=-j1 fixed it for me
Aside warnings like /usr/lib/python3.6/site-packages/numpy/distutils/system_info.py:1533: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /usr/lib/python3.6/site-packages/numpy/distutils/system_info.py:616: UserWarning: Specified path is invalid. warnings.warn('Specified path %s is invalid.' % d) Running from scipy source directory. /usr/lib/python3.6/site-packages/numpy/distutils/system_info.py:1632: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) I was able to build with MAKEOPTS=-j1
*** This bug has been marked as a duplicate of bug 614464 ***
