After upgrading cblas scipy fails during revdep-rebuild: $ sudo revdep-rebuild Password: * This is the new python coded version * Please report any bugs found using it. * The original revdep-rebuild script is installed as revdep-rebuild.sh * Please file bugs at: https://bugs.gentoo.org/ * Collecting system binaries and libraries * Checking dynamic linking consistency * Assign files to packages emerge --oneshot --complete-graph=y sci-libs/scipy:0 Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-libs/scipy-0.17.0::gentoo * scipy-0.17.0.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * Using following Fortran compiler: * F77: x86_64-pc-linux-gnu-gfortran * FC: x86_64-pc-linux-gnu-gfortran >>> Unpacking source... >>> Unpacking scipy-0.17.0.tar.gz to /var/tmp/portage/sci-libs/scipy-0.17.0/work >>> Source unpacked in /var/tmp/portage/sci-libs/scipy-0.17.0/work >>> Preparing source in /var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0 ... 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 * Applying scipy-0.12.0-blitz.patch ... [ ok ] * Applying scipy-0.12.0-restore-sys-argv.patch ... [ ok ] * Will copy sources from /var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0 * python2_7: copying to /var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0-python2_7 * python3_4: copying to /var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0-python3_4 >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0 ... * python2_7: running distutils-r1_run_phase python_compile Processing scipy/io/matlab/streams.pyx Processing scipy/io/matlab/mio5_utils.pyx Processing scipy/io/matlab/mio_utils.pyx Processing scipy/stats/vonmises_cython.pyx Processing scipy/stats/_rank.pyx Processing scipy/cluster/_vq.pyx Processing scipy/cluster/_hierarchy.pyx Processing scipy/signal/_max_len_seq_inner.pyx Processing scipy/signal/_spectral.pyx Processing scipy/interpolate/_ppoly.pyx Processing scipy/interpolate/interpnd.pyx Processing scipy/special/_ufuncs.pyx Processing scipy/special/_ufuncs_cxx.pyx Processing scipy/special/_ellip_harm_2.pyx Processing scipy/ndimage/src/_ni_label.pyx Processing scipy/spatial/ckdtree.pyx Processing scipy/spatial/qhull.pyx Processing scipy/sparse/_csparsetools.pyx.in Processing scipy/sparse/csgraph/_tools.pyx Processing scipy/sparse/csgraph/_traversal.pyx Processing scipy/sparse/csgraph/_reordering.pyx Processing scipy/sparse/csgraph/_min_spanning_tree.pyx Processing scipy/sparse/csgraph/_shortest_path.pyx Processing scipy/optimize/_group_columns.pyx Processing scipy/optimize/_lsq/givens_elimination.pyx 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 /usr/bin/python2.7 setup.py build -j 5 config_fc --noopt --noarch /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'setup_requires' warnings.warn(msg) /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) lapack_opt_info: system_info: NOT AVAILABLE /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:1526: 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__) 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:1549: 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. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /usr/lib64/python2.7/site-packages/numpy/distutils/system_info.py:1552: 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. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE Running from scipy source directory. Traceback (most recent call last): File "setup.py", line 265, in <module> setup_package() File "setup.py", line 262, 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 182, in configuration config.add_subpackage('scipy') File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage caller_level = 2) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, 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 1003, in add_subpackage caller_level = 2) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage caller_level = caller_level + 1) File "/usr/lib64/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/linalg/setup.py", line 20, in configuration raise NotFoundError('no lapack/blas resources found') numpy.distutils.system_info.NotFoundError: no lapack/blas resources found * ERROR: sci-libs/scipy-0.17.0::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 115: Called src_compile * environment, line 4247: Called distutils-r1_src_compile * environment, line 1250: Called _distutils-r1_run_foreach_impl 'python_compile' * environment, line 376: Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile' * environment, line 3666: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2740: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2738: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' * environment, line 833: Called distutils-r1_run_phase 'python_compile' * environment, line 1243: Called python_compile * environment, line 3254: Called distutils-r1_python_compile '-j' '5' 'config_fc' '--noopt' '--noarch' * environment, line 1118: Called esetup.py 'build' '-j' '5' 'config_fc' '--noopt' '--noarch' * environment, line 1749: Called die * The specific snippet of code: * "${@}" || die "${die_args[@]}"; * * If you need support, post the output of `emerge --info '=sci-libs/scipy-0.17.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.17.0::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.17.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.17.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0-python2_7' * S: '/var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0' >>> Failed to emerge sci-libs/scipy-0.17.0 * Messages for package sci-libs/scipy-0.17.0: * ERROR: sci-libs/scipy-0.17.0::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 115: Called src_compile * environment, line 4247: Called distutils-r1_src_compile * environment, line 1250: Called _distutils-r1_run_foreach_impl 'python_compile' * environment, line 376: Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile' * environment, line 3666: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2740: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 2738: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' * environment, line 833: Called distutils-r1_run_phase 'python_compile' * environment, line 1243: Called python_compile * environment, line 3254: Called distutils-r1_python_compile '-j' '5' 'config_fc' '--noopt' '--noarch' * environment, line 1118: Called esetup.py 'build' '-j' '5' 'config_fc' '--noopt' '--noarch' * environment, line 1749: Called die * The specific snippet of code: * "${@}" || die "${die_args[@]}"; * * If you need support, post the output of `emerge --info '=sci-libs/scipy-0.17.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.17.0::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.17.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.17.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0-python2_7' * S: '/var/tmp/portage/sci-libs/scipy-0.17.0/work/scipy-0.17.0' $ emerge --info Portage 2.3.1 (python 3.4.5-final-0, default/linux/amd64/13.0/systemd, gcc-5.4.0, glibc-2.23-r2, 4.7.5-gentoo x86_64) ================================================================= System uname: Linux-4.7.5-gentoo-x86_64-Intel-R-_Core-TM-_i7-6600U_CPU_@_2.60GHz-with-gentoo-2.3 KiB Mem: 16333248 total, 4649452 free KiB Swap: 33554428 total, 33277648 free Timestamp of repository gentoo: Fri, 30 Sep 2016 17:00:01 +0000 sh bash 4.4 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 app-shells/bash: 4.4::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo dev-util/cmake: 3.6.2::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 5.4.0::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 local-crossdev location: /usr/local/portage-crossdev masters: gentoo priority: 10 mlen location: /var/lib/layman/mlen masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=broadwell -mclflushopt -mxsavec -mxsaves -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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=broadwell -mclflushopt -mxsavec -mxsaves -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs cgroup config-protect-if-modified distlocks ebuild-locks fail-clean fixlafiles merge-sync 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.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5 -l5" 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 X509 aac aacplus acl alsa amd64 audit berkdb bzip2 caps cgroups cli cracklib crypt cryptsetup cups cxx dbus dri dri3 faac flac fortran gdbm geoclue geoloc geolocation gif gnome-keyring gtk gtk3 gtkstyle hidpi hotwording iconv idn infinality introspection iproute2 ipv6 jpeg kerberos libedit libnotify llvm lvm mbim mmx mmxext modemmanager modules mp3 mpeg multilib ncurses networkmanager nls nptl offensive ogg opengl openmp opus oss pam pch pcre png policykit pulseaudio python qt5 readline samba seccomp session sound sse sse2 ssl startup-notification systemd tcpd theora tiff truetype udev udisks unicode unwind vaapi vim-syntax virt-network vorbis vpx webp widgets x264 xattr xft xinerama zlib zsh-completion" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="synaptics evdev" KERNEL="linux" L10N="en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="x86_64 i386 arm" QEMU_USER_TARGETS="x86_64 i386 arm" RUBY_TARGETS="ruby23 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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, USE_PYTHON
Getting the same error here with 0.16.1.
Putting libraries = cblas in the various site.cfg files makes the compile go further but then it fails to link the first so file.
# eselect cblas set 1 Fixed the issue for me
(In reply to Harris Landgarten from comment #3) > # eselect cblas set 1 > > Fixed the issue for me Unfortunately not for me. # for i in blas cblas lapack; do eselect "$i" show; done lib64: reference lib64: reference lib64: reference
The eselect symlink to the cblas.pc file was incorrect in the lastest cblas version. Can you please try again with cblas-reference version 20151113-r2? commit ec07bd6704edd93082d57c41c7edf461e46cbe58 Author: Matthias Maier <tamiko@gentoo.org> Date: Sun Oct 9 10:22:44 2016 -0500 sci-libs/cblas-reference: fix eselect symlnk to pc file Package-Manager: portage-2.3.0
(In reply to Matthias Maier from comment #5) > The eselect symlink to the cblas.pc file was incorrect in the lastest cblas > version. Can you please try again with cblas-reference version 20151113-r2? > > > commit ec07bd6704edd93082d57c41c7edf461e46cbe58 > Author: Matthias Maier <tamiko@gentoo.org> > Date: Sun Oct 9 10:22:44 2016 -0500 > > sci-libs/cblas-reference: fix eselect symlnk to pc file > > Package-Manager: portage-2.3.0 Had to get this manually (mirror slowly updating?), but it does make everything work.
Works for me as well
(In reply to Matthias Maier from comment #5) > The eselect symlink to the cblas.pc file was incorrect in the lastest cblas > version. Can you please try again with cblas-reference version 20151113-r2? It's completely broken on prefix. Look at the 20151113-r2 ebuild: mkdir -p "${ED}/usr/$(get_libdir)/blas/reference" || die mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/include"/cblas* \ "${ED}/usr/$(get_libdir)/pkgconfig"/* \ "${ED}/usr/$(get_libdir)/blas/reference" || die rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die rmdir "${ED}/usr/include" || die rm -rf "${ED}"/usr/lib/ || die See what happens when $(get_libdir) == "lib" (which is the case on prefix)? All the files you are installing in "${ED}/usr/$(get_libdir)/blas/reference will get wiped out by the "rm -rf" :))
(In reply to Alexandre Rostovtsev from comment #8) > (In reply to Matthias Maier from comment #5) > > The eselect symlink to the cblas.pc file was incorrect in the lastest cblas > > version. Can you please try again with cblas-reference version 20151113-r2? > > It's completely broken on prefix. Look at the 20151113-r2 ebuild: > > mkdir -p "${ED}/usr/$(get_libdir)/blas/reference" || die > mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/include"/cblas* \ > "${ED}/usr/$(get_libdir)/pkgconfig"/* \ > "${ED}/usr/$(get_libdir)/blas/reference" || die > > rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die > rmdir "${ED}/usr/include" || die > rm -rf "${ED}"/usr/lib/ || die > > See what happens when $(get_libdir) == "lib" (which is the case on prefix)? That's correct. Not only on prefix but also for i686, arm, etc. > All the files you are installing in "${ED}/usr/$(get_libdir)/blas/reference > will get wiped out by the "rm -rf" :)) Yup.
Wow. I cleaned up sci-libs/blas-reference but apparently forgot cblas. commit aca8ce1ed089c80e40dbb6aa922ef70e45ac2eb9 Author: Matthias Maier <tamiko@gentoo.org> Date: Tue Oct 25 20:27:46 2016 -0500 sci-libs/cblas-reference: do not remove /usr/lib, bug #596036, bug #597288 Non non-amd64 systems "$(get_libdir)" might actually be "lib". So do not blindly delete this folder. Package-Manager: portage-2.3.0
*** Bug 546858 has been marked as a duplicate of this bug. ***
