* python3_6: running distutils-r1_run_phase python_compile python3.6 setup.py build -j 1 config_fc --noopt --noarch --fcompiler=gnu95 blas_opt_info: system_info: NOT AVAILABLE accelerate_info: NOT AVAILABLE blas_info: customize UnixCCompiler customize UnixCCompiler C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -flto=4 -fuse-linker-plugin -O2 -pipe -march=native -flto=4 -fuse-linker-plugin -fno-strict-aliasing -fPIC creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp/portage creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp/portage/dev-python creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp/portage/dev-python/numpy-1.17.4 creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp/portage/dev-python/numpy-1.17.4/temp creating /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua compile options: '-I -I/usr/include -c' x86_64-pc-linux-gnu-gcc: /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/source.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -flto=4 -fuse-linker-plugin /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/source.o -L/usr/lib64 -lblas -lcblas -o /var/tmp/portage/dev-python/numpy-1.17.4/temp/tmpeyz2xqua/a.out FOUND: libraries = [['blas', 'cblas']] library_dirs = ['/usr/lib64'] include_dirs = ['', '/usr/include'] language = c define_macros = [('HAVE_CBLAS', None)] FOUND: define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] libraries = [['blas', 'cblas']] library_dirs = ['/usr/lib64'] include_dirs = ['', '/usr/include'] language = c /bin/sh: svnversion: command not found lapack_opt_info: flame_info: customize UnixCCompiler libraries flame not found in ['/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/'] NOT AVAILABLE lapack_info: customize UnixCCompiler FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib64'] language = f77 FOUND: libraries = ['lapack', ['blas', 'cblas']] library_dirs = ['/usr/lib64'] language = c define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)] include_dirs = ['', '/usr/include'] running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options Running from numpy source directory. /var/tmp/portage/dev-python/numpy-1.17.4/work/numpy-1.17.4/numpy/distutils/system_info.py:669: UserWarning: Optimized (vendor) Blas libraries are not found. Falls back to netlib Blas library which has worse performance. A better performance should be easily gained by switching Blas library. self.calc_info() /usr/lib64/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) error: second element of each tuple in 'libraries' must be a dictionary (build info) * ERROR: dev-python/numpy-1.17.4::gentoo failed (compile phase): * (no error message)
Portage 2.3.79 (python 3.6.9-final-0, default/linux/amd64/17.0, gcc-9.2.0, glibc-2.30-r2, 5.2.13-gentoo x86_64) ================================================================= System uname: Linux-5.2.13-gentoo-x86_64-AMD_FX-tm-8350_Eight-Core_Processor-with-gentoo-2.6 KiB Mem: 32928272 total, 12761096 free KiB Swap: 0 total, 0 free sh bash 5.0_p11 ld GNU ld (Gentoo 2.32 p2) 2.32.0 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, 3.6.9::gentoo dev-util/cmake: 3.15.5::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-r4::gentoo sys-devel/automake: 1.16.1-r2::gentoo sys-devel/binutils: 2.32-r1::gentoo, 2.33.1::gentoo sys-devel/gcc: 9.2.0-r2::gentoo sys-devel/gcc-config: 2.1::gentoo sys-devel/libtool: 2.4.6-r5::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 5.3-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.30-r2::gentoo Repositories: gentoo location: /home/me/code/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: no adjust location: /home/me/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 -flto=4 -fuse-linker-plugin" 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="-O2 -pipe -march=native -flto=4 -fuse-linker-plugin" DISTDIR="/chroot/distfiles" 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 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://distfiles.gentoo.org" INSTALL_MASK="/etc/X11/xinit/xinitrc.d/80-dbus /usr/bin/dbus-launch" LANG="en_US.utf8" LDFLAGS="-O2 -flto=4" 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 multilib ncurses nls nptl opencl opengl openmp pam pcre pgo readline seccomp split-usr sqlite ssl tcpd truetype udev unicode vdpau vulkan xattr xvmc 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="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 greis 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" 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_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby25" 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, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Message -- error: second element of each tuple in 'libraries' must be a dictionary (build info) -- comes from /usr/lib/python3.*/distutils/command/build_clib.py from "def check_library_list(self, libraries)" from loop "for lib in libraries:" On my system "libraries" is list of 3 elem: [('npymath', {'include_dirs': [], ... 'depends': []}), ('npysort', {'include_dirs': [], ... 'depends': []}), ('blas', 'cblas')] last string -- 'cblas' -- is obviously not dictionary In my desperate daring I patched distutils/command/build_clib.py to replace 'cblas' with {'include_dirs': [], 'depends': []} and it worked.
And now it's /usr/lib/python3.8/site-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so: undefined symbol: cblas_dsyrk
I was able to build numpy-1.17.4 reverting the no-hardcoded-blas patch: # ebuild `equery w numpy` clean prepare # patch -RNp1 -i /var/db/repos/gentoo/dev-python/numpy/files/numpy-1.17.4-no-hardcode-blas.patch -d /var/tmp/portage/dev-python/numpy-1.17.4/work/numpy-1.17.4/ # ebuild `equery w numpy` merge clean On a side note: on my system(s), the generated site.cfg looks bizarre (to me) because of the presence of colons: cat site.cfg [blas] include_dirs = :/usr/include library_dirs = :/usr/lib64 blas_libs = blas,cblas [lapack] library_dirs = :/usr/lib64 lapack_libs = lapack Is that the expected result? Additional info On my systems, sci-libs/lapack-3.8.0:0, sci-libs/openblas-0.3.7:0, virtual/blas-3.8:0, virtual/cblas-3.8:0 and virtual/lapack-3.8 are built with USE=eselect-ldso
Right, the patch is maybe buggy.
The last segment of the patch can be removed, the compile will then succeed. The call to pc_incdir() should be removed, as $(pkg-config --cflags-only-I) is empty for blas, cblas and lapack. The call to pc_libdir() should be removed, as $(pkg-config --libs-only-L) is empty for blas, cblas and lapack.
Fixed in 817df86ab2fc967c40f1d2abe50a43bab24917df
*** Bug 702328 has been marked as a duplicate of this bug. ***
(In reply to Patrick Lauer from comment #7) > Fixed in 817df86ab2fc967c40f1d2abe50a43bab24917df Patrick, what was your motivation making the following change along with the patch update? There are needed for numpy on Prefix to locate the correct locations of blas and lapack. @@ -74,11 +74,8 @@ local libdir="${EPREFIX}"/usr/$(get_libdir) cat >> site.cfg <<-EOF || die [blas] - include_dirs = $(pc_incdir cblas):${incdir} - library_dirs = $(pc_libdir cblas blas):${libdir} blas_libs = $(pc_libs cblas blas) [lapack] - library_dirs = $(pc_libdir lapack):${libdir} lapack_libs = $(pc_libs lapack) EOF else
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=261f747b27a57db8c9da8fc9f2d1a991a5db350e commit 261f747b27a57db8c9da8fc9f2d1a991a5db350e Author: Benda Xu <heroxbd@gentoo.org> AuthorDate: 2020-01-25 03:20:43 +0000 Commit: Benda Xu <heroxbd@gentoo.org> CommitDate: 2020-01-25 03:24:56 +0000 dev-python/numpy: replace pc_incdir() with plain names. Same goes to pc_libs() and pc_libdir(). pkg-config mechanism is not necessary any more with the introduction of eselect-ldso. All the compile and linking time operation are done against standard blas and lapack headers and libraries. Closes: https://bugs.gentoo.org/700848 Package-Manager: Portage-2.3.79, Repoman-2.3.18 Signed-off-by: Benda Xu <heroxbd@gentoo.org> dev-python/numpy/numpy-1.17.4-r2.ebuild | 139 ++++++++++++++++++++++++++++++++ 1 file changed, 139 insertions(+)
*** Bug 519984 has been marked as a duplicate of this bug. ***
