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Bug 664890 - dev-python/pandas-0.23.4 - ImportError: cannot open shared object file
Summary: dev-python/pandas-0.23.4 - ImportError: cannot open shared ...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2018-08-30 14:31 UTC by Juergen Rose
Modified: 2019-12-23 10:12 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---

build.log (build.log,98.54 KB, text/x-log)
2018-08-30 14:31 UTC, Juergen Rose
build.log for sage (build.log,10.29 KB, text/x-log)
2018-09-04 21:47 UTC, Juergen Rose

Note You need to log in before you can comment on or make changes to this bug.
Description Juergen Rose 2018-08-30 14:31:35 UTC
Created attachment 545508 [details]

'MAKEOPTS=-j1 emerge -v1 pandas' fails with:
UPDATING /var/tmp/portage/dev-python/pandas-0.23.4/work/pandas-0.23.4-python2_7/lib/pandas/
set /var/tmp/portage/dev-python/pandas-0.23.4/work/pandas-0.23.4-python2_7/lib/pandas/ to '0.23.4'
running build_ext
Traceback (most recent call last):
  File "", line 749, in <module>
  File "/usr/lib64/python2.7/site-packages/setuptools/", line 131, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib64/python2.7/distutils/", line 151, in setup
  File "/usr/lib64/python2.7/distutils/", line 953, in run_commands
  File "/usr/lib64/python2.7/distutils/", line 972, in run_command
  File "/usr/lib64/python2.7/distutils/command/", line 127, in run
  File "/usr/lib64/python2.7/distutils/", line 326, in run_command
  File "/usr/lib64/python2.7/distutils/", line 972, in run_command
  File "/usr/lib64/python2.7/site-packages/Cython/Distutils/", line 186, in run
  File "/usr/lib64/python2.7/distutils/command/", line 340, in run
  File "", line 378, in build_extensions
  File "", line 128, in build_extensions
    numpy_incl = pkg_resources.resource_filename('numpy', 'core/include')
  File "/usr/lib64/python2.7/site-packages/pkg_resources/", line 1135, in resource_filename
    return get_provider(package_or_requirement).get_resource_filename(
  File "/usr/lib64/python2.7/site-packages/pkg_resources/", line 351, in get_provider
  File "/usr/lib64/python2.7/site-packages/numpy/", line 142, in <module>
    from . import add_newdocs
  File "/usr/lib64/python2.7/site-packages/numpy/", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/lib64/python2.7/site-packages/numpy/lib/", line 19, in <module>
    from .polynomial import *
  File "/usr/lib64/python2.7/site-packages/numpy/lib/", line 20, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/usr/lib64/python2.7/site-packages/numpy/linalg/", line 51, in <module>
    from .linalg import *
  File "/usr/lib64/python2.7/site-packages/numpy/linalg/", line 31, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: cannot open shared object file: No such file or directory
 * ERROR: dev-python/pandas-0.23.4::gentoo failed (compile phase):

root@lynx:/root(18)# updatedb;  locate

root@lynx:/root(19)# emerge --info '=dev-python/pandas-0.23.4::gentoo'
Portage 2.3.48 (python 3.6.6-final-0, default/linux/amd64/17.0/desktop, gcc-8.2.0, glibc-2.27-r6, 4.18.5-gentoo x86_64)
                         System Settings
System uname: Linux-4.18.5-gentoo-x86_64-Intel-R-_Core-TM-_i7-6700HQ_CPU_@_2.60GHz-with-gentoo-2.6
KiB Mem:    15905064 total,   2235484 free
KiB Swap:   50331644 total,  49408044 free
Timestamp of repository gentoo: Thu, 30 Aug 2018 14:00:01 +0000
Head commit of repository gentoo: 49512f725812ef1c80a186e6bea965980025ec37
sh bash 4.4_p23
ld GNU ld (Gentoo 2.30 p3) 2.30.0
distcc[11756] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Mar 21 2018 07:00:29 [disabled]
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-r100::sage-on-gentoo, 3.6.6::gentoo, 3.7.0::gentoo
dev-util/cmake:           3.11.4-r1::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::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, 1.13.4-r2::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils:       2.30-r3::gentoo, 2.31.1::gentoo
sys-devel/gcc:            8.2.0-r2::gentoo
sys-devel/gcc-config:     2.0::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 4.17::gentoo (virtual/os-headers)
sys-libs/glibc:           2.27-r6::gentoo

    location: /usr/portage_lynx
    sync-type: rsync
    sync-uri: rsync://
    priority: -1000
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-max-age: 24

    location: /usr/local/portage
    masters: gentoo
    priority: 0

    location: /var/lib/cpan
    masters: gentoo
    priority: 1

    location: /var/lib/g-octave
    masters: gentoo
    priority: 2

    location: /var/lib/layman/ago
    masters: gentoo
    priority: 50

    location: /var/lib/layman/imaging
    masters: gentoo
    priority: 50

    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 50

    location: /var/lib/layman/science
    masters: gentoo
    priority: 50

    location: /var/lib/layman/tlp
    masters: gentoo
    priority: 50

    location: /var/lib/layman/torbrowser
    masters: gentoo
    priority: 50

    location: /var/lib/layman/x11
    masters: gentoo
    priority: 50

Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype- googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CFLAGS="-march=broadwell -O2 -pipe"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /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/php/apache2-php7.2/ext-active/ /etc/php/cgi-php7.2/ext-active/ /etc/php/cli-php7.2/ext-active/ /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 -O2 -pipe"
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="-march=broadwell -O2 -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de en fr ru"
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"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audiofile aufs automap automount barcode bash-completion berkdb blas blast bluetooth bluray boost branding btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cilk clang cli cmake collada consolekit contrib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia digitalradio djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evdev evo examples excel exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse gcj gd gdal gdbm gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jadetex java jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate libtirpc live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg opencv openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds ppp preview-latex proj projectm pstricks pulseaudio python q16 q32 qemu qhull qml qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tbb tcl tcpd tex tex4ht theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video vim-syntax virt-network virtualbox visio vorbis vpx vtk wav wayland webdav webdav-serf webkit wifi wmf wxwidgets x264 x265 xa xattr xcb xen xetex xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zsh-completion zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="karbon plan sheets stage words" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="aes avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 navcom ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf superstar2 tnt tripmate tsip ublox nmea0183 nmea2000 passthrough" GRUB_PLATFORMS="emu efi-64 pc xen" INPUT_DEVICES="keyboard mouse evdev synaptics void" KERNEL="linux" L10N="de en fr ru" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LIRC_DEVICES="devinput" LLVM_TARGETS="NVPTX X86" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" 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="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby23" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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"

                        Package Settings

dev-python/pandas-0.23.4::gentoo was built with the following:
USE="doc -X -full-support -minimal -test" ABI_X86="(64)" PYTHON_TARGETS="python2_7 python3_6 -python3_5"

root@lynx:/root(20)# emerge -pqv '=dev-python/pandas-0.23.4::gentoo'
[ebuild   R   ] dev-python/pandas-0.23.4  USE="X* doc -full-support -minimal -test" PYTHON_TARGETS="python2_7 python3_6 -python3_5"
Comment 1 François Bissey 2018-08-30 21:12:10 UTC
gcc-8 is your culprit. There was a bump from to in gcc-7, we now have a bump to in gcc-8.

All the bugs we had opened before because blas/lapack where linked to and gcc-7 was trying to link will appear once more with an increment.

revdep-rebuild --library '' -- --exclude gcc

before trying to merge pandas again.
Comment 2 Juergen Rose 2018-09-04 21:29:01 UTC
(In reply to François Bissey from comment #1)
> gcc-8 is your culprit. There was a bump from to
> in gcc-7, we now have a bump to in gcc-8.
> All the bugs we had opened before because blas/lapack where linked to
> and gcc-7 was trying to link will appear
> once more with an increment.
> Try
> revdep-rebuild --library '' -- --exclude gcc
> before trying to merge pandas again.

'revdep-rebuild --library '' -- --exclude gcc' seems not to be enough to solve the problem. I have here the next similar problem, 'emerge sage' fails, but a subsequent revdep-rebuild does not detect

ImportError: cannot open shared object file: No such file or directory
Error building the Sage library

>>> Failed to emerge sci-mathematics/sage-8.3-r1, Log file:

>>>  '/var/log/portage/sci-mathematics:sage-8.3-r1:20180902-163052.log'
root@lynxold:/usr/local/portage/sci-geosciences(38)# revdep-rebuild --library '' -- --exclude gcc
 * This is the new python coded version
 * Please report any bugs found using it.
 * The original revdep-rebuild script is installed as
 * Please file bugs at:
 * Collecting system binaries and libraries
 * Checking dynamic linking consistency

Your system is consistent
Comment 3 François Bissey 2018-09-04 21:30:58 UTC
If you give me a bit more of the sage build log I may be able to figure out what's been missed.
Comment 4 Juergen Rose 2018-09-04 21:45:49 UTC
(In reply to François Bissey from comment #3)
> If you give me a bit more of the sage build log I may be able to figure out
> what's been missed.

I assume that atlas is responsible for this issue:
root@lynxold:/usr/local/portage/sci-geosciences(40)# genlop -t atlas | tail

     Mon Jan  1 15:26:46 2018 >>> sci-libs/atlas-3.11.39
       merge time: 2 hours, 10 minutes and 44 seconds.

     Wed Jan  3 06:00:13 2018 >>> sci-libs/atlas-3.11.39
       merge time: 2 hours, 39 minutes and 32 seconds.

     Sun Aug 12 15:27:11 2018 >>> sci-libs/atlas-3.11.39
       merge time: 3 hours, 8 minutes and 43 seconds.

root@lynxold:/usr/local/portage/sci-geosciences(41)# genlop -t gcc | tail

     Sun May 20 08:44:23 2018 >>> sys-devel/gcc-7.3.0-r3
       merge time: 57 minutes and 29 seconds.

     Mon Jun 25 11:52:29 2018 >>> sys-devel/gcc-7.3.0-r3
       merge time: 59 minutes and 16 seconds.

     Sun Aug 19 21:21:38 2018 >>> sys-devel/gcc-8.2.0-r2
       merge time: 1 hour, 31 minutes and 12 seconds.
Comment 5 Juergen Rose 2018-09-04 21:47:03 UTC
Created attachment 545940 [details]
build.log for sage
Comment 6 François Bissey 2018-09-04 21:47:58 UTC
Right, that would fit since f77blas and lapack from atlas link to libgfortran.
Comment 7 François Bissey 2018-09-04 21:52:43 UTC
And the log you give basically say that numpy tries to open and the only way that should happen is through lapack.
If revdep-rebuild doesn't work you'll have to do is 
1) rebuild you blas implementations.
2) rebuild the matching lapack implementation (if not covered by (1)).
3) rebuild all the dependencies has given by `equery d blas lapack`
Comment 8 Benda Xu gentoo-dev 2019-12-23 10:12:41 UTC
I think this bug has been fixed by bug 646090.