Created attachment 543228 [details] Output of compilation and installation of dev-python/numpy-1.10.4 I did an emerge -DuvaN @world, which brought with it a recompile of dev-python/numpy-1.10.4. Some of the C files didn't compile, but emerge didn't seem to notice this, so went ahead and installed this partial Numpy build. Later, another package, dev-python/bottleneck-1.0.0, in the same @world update failed in an "import numpy" statement, and emerge did notice this. The final error message from emerge therefore focuses on Bottleneck, but the real problem seems to be with Numpy. The whole emerge -DuvaN @world was quite large this time, but I have saved a copy of the complete output of the whole thing. For now, I think the output of the Numpy compile and install should be enough.
$ sudo emerge --info '=dev-python/numpy-1.10.4::gentoo' Password: Portage 2.3.40 (python 3.5.5-final-0, default/linux/amd64/17.0/desktop/gnome/systemd, gcc-6.4.0, glibc-2.26-r7, 4.9.95-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.9.95-gentoo-x86_64-Intel-R-_Core-TM-_i7-6700HQ_CPU_@_2.60GHz-with-gentoo-2.4.1 KiB Mem: 32762124 total, 7301776 free KiB Swap: 33558524 total, 33558524 free Timestamp of repository gentoo: Sat, 11 Aug 2018 22:00:01 +0000 Head commit of repository gentoo: bd87a494675a7ef194d6980a30afb8e944328156 sh bash 4.4_p12 ld GNU ld (Gentoo 2.29.1 p3) 2.29.1 app-shells/bash: 4.4_p12::gentoo dev-lang/perl: 5.24.3-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.5.5::gentoo, 3.6.5::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/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.15.1-r2::gentoo sys-devel/binutils: 2.29.1-r1::gentoo, 2.30-r2::gentoo sys-devel/gcc: 6.4.0-r1::gentoo, 7.3.0-r3::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1-r3::gentoo sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 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/libreoffice/program/sofficerc /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="-march=native -O2 -pipe" DISTDIR="/usr/portage/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://trumpetti.atm.tut.fi/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo http://mirror.mdfnet.se/gentoo" LANG="en_GB.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j7" 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 acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord crypt cxx dbus dri dts dvd dvdr eds emboss encode evo exif fam flac fortran gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk iconv introspection ipv6 jpeg lcms ldap libnotify libsecret libtirpc mad mmx mng modules mp3 mp4 mpeg multilib nautilus ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio readline sdl seccomp spell sse sse2 ssl startup-notification svg systemd tcpd tiff tracker truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xml xv xvid 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" 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" GRUB_PLATFORMS="efi-64" 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="ruby23" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-python/numpy-1.10.4::gentoo was built with the following: USE="lapack -doc -test" ABI_X86="(64)" PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5" CFLAGS="-march=native -O2 -pipe -fno-strict-aliasing" CXXFLAGS="-march=native -O2 -pipe -fno-strict-aliasing" LDFLAGS="-Wl,-O1 -Wl,--as-needed -shared" $ sudo emerge -pqv '=dev-python/numpy-1.10.4::gentoo' [ebuild R ] dev-python/numpy-1.10.4 USE="lapack -doc {-test}" PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5"
This was a misunderstanding on my part. Resolving my own bug as invalid.
