| Summary: | sci-libs/scipy-1.0.0 - /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:552: UserWarning: {Atlas/Blas} libraries not found. | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Fabio Coatti <fabio.coatti> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | dominique.c.michel, frp.bissey, zeekec |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
Did you just upgrade to gcc 7.2.0? I suspect you are a victim of the so bump in libgfortran. In that case you may have to do the following emerge -1v $your_blas emerge -1v $your_lapack emerge -1v numpy and then see if scipy can be built. Done the following: emerge -1 sci-libs/blas-reference emerge -1v sci-libs/lapack-reference emerge -1v numpy MAKEOPTS=-j1 emerge -1 sci-libs/scipy Still no luck >>> Emerging (1 of 1) sci-libs/scipy-1.0.0::gentoo * scipy-1.0.0.tar.gz BLAKE2B SHA512 size ;-) ... [ ok ] >>> cfg-update-1.8.2-r1: Checksum index is up-to-date ... * Using following Fortran compiler: * F77: x86_64-pc-linux-gnu-gfortran * FC: x86_64-pc-linux-gnu-gfortran >>> Unpacking source... >>> Unpacking scipy-1.0.0.tar.gz to /var/tmp/portage/sci-libs/scipy-1.0.0/work >>> Source unpacked in /var/tmp/portage/sci-libs/scipy-1.0.0/work >>> Preparing source in /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0 ... Package cblas was not found in the pkg-config search path. Perhaps you should add the directory containing `cblas.pc' to the PKG_CONFIG_PATH environment variable No package 'cblas' found Package cblas was not found in the pkg-config search path. Perhaps you should add the directory containing `cblas.pc' to the PKG_CONFIG_PATH environment variable No package 'cblas' found Package cblas was not found in the pkg-config search path. Perhaps you should add the directory containing `cblas.pc' to the PKG_CONFIG_PATH environment variable No package 'cblas' found * Will copy sources from /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0 * python2_7: copying to /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0-python2_7 * python3_4: copying to /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0-python3_4 * python3_5: copying to /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0-python3_5 * python3_6: copying to /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0-python3_6 >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0 ... * python2_7: running distutils-r1_run_phase python_compile scipy/linalg/_generate_pyx.py: all files up-to-date scipy/special/_generate_pyx.py: all files up-to-date Running scipy/linalg/_generate_pyx.py Running scipy/special/_generate_pyx.py Processing scipy/linalg/_decomp_update.pyx.in Processing scipy/linalg/cython_lapack.pyx Processing scipy/linalg/cython_blas.pyx Processing scipy/linalg/_solve_toeplitz.pyx Processing scipy/signal/_spectral.pyx Processing scipy/signal/_max_len_seq_inner.pyx Processing scipy/signal/_upfirdn_apply.pyx Processing scipy/optimize/_group_columns.pyx Processing scipy/optimize/_trlib/_trlib.pyx Processing scipy/optimize/_lsq/givens_elimination.pyx Processing scipy/stats/_stats.pyx Processing scipy/interpolate/_ppoly.pyx Processing scipy/interpolate/_bspl.pyx Processing scipy/interpolate/interpnd.pyx Processing scipy/sparse/_csparsetools.pyx.in Processing scipy/sparse/csgraph/_traversal.pyx Processing scipy/sparse/csgraph/_tools.pyx Processing scipy/sparse/csgraph/_min_spanning_tree.pyx Processing scipy/sparse/csgraph/_reordering.pyx Processing scipy/sparse/csgraph/_shortest_path.pyx Processing scipy/io/matlab/mio5_utils.pyx Processing scipy/io/matlab/mio_utils.pyx Processing scipy/io/matlab/streams.pyx Processing scipy/ndimage/src/_cytest.pyx Processing scipy/ndimage/src/_ni_label.pyx Processing scipy/spatial/qhull.pyx Processing scipy/spatial/_voronoi.pyx Processing scipy/spatial/_hausdorff.pyx Processing scipy/spatial/ckdtree.pyx Processing scipy/cluster/_vq.pyx Processing scipy/cluster/_optimal_leaf_ordering.pyx Processing scipy/cluster/_hierarchy.pyx Processing scipy/special/_test_round.pyx Processing scipy/special/cython_special.pyx Processing scipy/special/_ufuncs.pyx Processing scipy/special/_ellip_harm_2.pyx Processing scipy/special/_comb.pyx Processing scipy/special/_ufuncs_cxx.pyx Processing scipy/_lib/messagestream.pyx Processing scipy/_lib/_ccallback_c.pyx /usr/bin/python2.7 setup.py build config_fc --noopt --noarch lapack_opt_info: system_info: NOT AVAILABLE /usr/lib64/python2.7/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() lapack_info: FOUND: libraries = ['blas', 'lapack'] library_dirs = ['/usr/lib64'] language = f77 blas_info: libraries not found in ['', '/usr/lib64'] NOT AVAILABLE /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:552: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. self.calc_info() blas_src_info: NOT AVAILABLE /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:552: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. self.calc_info() NOT AVAILABLE Running from scipy source directory. Traceback (most recent call last): File "setup.py", line 418, in <module> setup_package() File "setup.py", line 414, in setup_package setup(**metadata) File "/usr/lib64/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 336, in configuration config.add_subpackage('scipy') File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 1029, in add_subpackage caller_level = 2) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 998, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 15, in configuration config.add_subpackage('linalg') File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 1029, in add_subpackage caller_level = 2) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 998, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/linalg/setup.py", line 19, in configuration raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found * ERROR: sci-libs/scipy-1.0.0::gentoo failed (compile phase): * (no error message) It looks like your system is not set up properly. Did you eselect blas-reference and lapack-reference properly? Well, the output is the following: hobbes ~ # eselect lapack show lib64: reference hobbes ~ # eselect blas show lib64: reference Not really sure if this is enough If I trust the log you posted you are missing /usr/lib64/pkgconfig/cblas.pc. <slapping my face> hum, that means you also need a cblas for scipy, and that it must be properly set. So emerge -1v $your_cblas Thanks a lot, this indeed worked. Previousy I had no cblas package, eselect cblas was reporting gsl as configured provider. Forcing the installation of sci-libs/cblas-reference did the trick. Now I need only to understand what's really happened (I was expecting some missing dep complaint from scipy), but this is another story. Many thanks again. *** Bug 681954 has been marked as a duplicate of this bug. *** |
Trying to emerge scipy with the following command: MAKEOPTS=-j1 emerge -1 sci-libs/scipy I get this error (the following is basically the emerge log): Processing scipy/ndimage/src/_ni_label.pyx /usr/bin/python2.7 setup.py build config_fc --noopt --noarch lapack_opt_info: system_info: NOT AVAILABLE /usr/lib64/python2.7/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() lapack_info: FOUND: libraries = ['blas', 'lapack'] library_dirs = ['/usr/lib64'] language = f77 blas_info: libraries not found in ['', '/usr/lib64'] NOT AVAILABLE /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:552: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. self.calc_info() blas_src_info: NOT AVAILABLE /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:552: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. self.calc_info() NOT AVAILABLE Running from scipy source directory. Traceback (most recent call last): File "setup.py", line 418, in <module> setup_package() File "setup.py", line 414, in setup_package setup(**metadata) File "/usr/lib64/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 336, in configuration config.add_subpackage('scipy') File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 1029, in add_subpackage caller_level = 2) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 998, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 15, in configuration config.add_subpackage('linalg') File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 1029, in add_subpackage caller_level = 2) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 998, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/linalg/setup.py", line 19, in configuration raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found Reproducible: Always emerge --info Portage 2.3.16 (python 3.4.6-final-0, default/linux/amd64/17.0/desktop/plasma/systemd, gcc-7.2.0, glibc-2.26-r3, 4.14.4-cova x86_64) ================================================================= System uname: Linux-4.14.4-cova-x86_64-Intel-R-_Core-TM-_i7-6820HQ_CPU_@_2.70GHz-with-gentoo-2.4.1 KiB Mem: 65471312 total, 58469268 free KiB Swap: 8388604 total, 8388604 free Timestamp of repository gentoo: Wed, 06 Dec 2017 07:30:01 +0000 Head commit of repository gentoo: 896bdabc878a169847a76353834cbb802edb1a40 sh bash 4.4_p12 ld GNU ld (Gentoo 2.29.1 p2) 2.29.1 app-shells/bash: 4.4_p12::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.1-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.4.6-r1::gentoo, 3.5.4-r1::gentoo, 3.6.3-r1::gentoo dev-util/cmake: 3.10.0::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, 1.15.1-r1::gentoo sys-devel/binutils: 2.29.1-r1::gentoo sys-devel/gcc: 6.4.0::gentoo, 7.2.0::gentoo sys-devel/gcc-config: 1.9.0-r1::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r1::gentoo sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-extra-opts: kde location: /var/lib/layman/kde sync-type: laymansync sync-uri: https://github.com/gentoo/kde.git masters: gentoo priority: 50 pypi location: /var/lib/layman/pypi sync-type: laymansync sync-uri: gs-pypi pypi masters: gentoo priority: 50 torbrowser location: /var/lib/layman/torbrowser sync-type: laymansync sync-uri: https://github.com/MeisterP/torbrowser-overlay.git masters: gentoo priority: 50 local location: /usr/overlay masters: gentoo priority: 51 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -fpie -fpic -pipe -march=native -fstack-protector-strong -flto=4 -fuse-linker-plugin" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/sddm/scripts/Xsetup" 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 -fpie -fpic -pipe -march=native -fstack-protector-strong -flto=4 -fuse-linker-plugin" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs clean-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" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -O2 -fpie -fpic -pipe -march=native -fstack-protector-strong -flto=4 -fuse-linker-plugin" 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="3dnow 3dnowext 3dnowprefetch X \ a52 aac aalib acl acpi activities aim alsa amd64 apng appstream ares asf ati audio audiofile avahi bash-completion berkdb bidi bl bluetooth branding bri bzip2 cairo caps cdda cdr cjk cli cracklib crypt cups curl cxx dba dbus declarative device-mapper dga divx divx4linux dri dts dv dvb dvd dvdr dvdread eap-sim edl egl emboss encode ethereal evdev exif expat faad fam fame fbcon ffmpeg fftw firefox flac force-cgi-redirect fortran ftp gallium garmin gd gdbm gif gimp glamor gmedia gmp gnutls gphoto2 gpm gps gsm gtk h264 h323 iconv icq icu idn ifp ilbc imagemagick imap innodb ipod iproute2 ipv6 ithreads jabber java javascript joystick jpeg kde kipi kontact kvm kwallet lastfm lcms ldap libnotify libvirtd live lm_sensors lua lvm lxc lzma lzo mad maildir matroska mbox mdnsresponder-compat mhash mime mjpeg mmap mmx mmxext mng modules mozdevelop mozilla mp3 mp4 mpeg msn mtp multilib mysql ncurses network networkmanager new-hpcups nfsv4 njb nls nptl nptlonly nsplugin offensive ofx ogg oggvorbis ogm openal openexr opengl openmp oscar pam pango parted pcap pcre pdf phonon php plasma plotutils png policykit ppds pulseaudio qemu qml qt3support qt5 readline real rtc ruby samba sasl sdl seccomp semantic-desktop semantic-destkop session sha512 sip slang slp smartcard sndfile snmp sox speex spell srt sse sse2 ssh ssl ssse3 startup-notification svg symlink systemd tcltk tcpd telepathy theora threads tiff tk touchpad tremor truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vcd vde vdpaum vhosts video videos vim-syntax virt-network virtualbox vorbis vulkan wav wayland webkit widgets wifi wmf wmp wps wxwidgets wxwindows x264 xanim xattr xcb xcomposite xface xft xine xinerama xml xosd xpm xscreensaver xsl xv xvid zeroconf zlib zpm" 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="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 avx2 f16c fma3 mmx mmxext popcnt sse sse2 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" KERNEL="linux" L10N="en it de" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en it de" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby22 ruby23 ruby24" USERLAND="GNU" VIDEO_CARDS="i965 intel nvidia 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS