Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 644020 - sci-libs/scipy-1.0.0 needs <gcc-7 for (ImportError: cannot open shared object file)
Summary: sci-libs/scipy-1.0.0 needs <gcc-7 for (ImportError: libgfort...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Linux bug wranglers
: 681786 (view as bug list)
Depends on:
Blocks: gcc-7
  Show dependency tree
Reported: 2018-01-09 16:38 UTC by Kobboi
Modified: 2019-03-26 10:59 UTC (History)
4 users (show)

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

buidl.log (scipy-build.log,5.30 KB, text/x-log)
2018-02-01 20:31 UTC, Andrew Ammerlaan
emerge-info (scipy-emerge-info.txt,6.56 KB, text/plain)
2018-02-01 20:34 UTC, Andrew Ammerlaan
ebuild environment (scipy-environment.txt,155.55 KB, text/plain)
2018-02-01 20:35 UTC, Andrew Ammerlaan

Note You need to log in before you can comment on or make changes to this bug.
Description Kobboi 2018-01-09 16:38:31 UTC
Without gcc:6.4.0 and only gcc:72.0, the scipy build fails quite soon:

>>> Emerging (1 of 1) sci-libs/scipy-1.0.0::gentoo
 * scipy-1.0.0.tar.gz BLAKE2B SHA512 size ;-) ...                                                                                                      [ ok ]
 * 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 ...
 * 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_5: copying to /var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0-python3_5
>>> 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/ all files up-to-date
Traceback (most recent call last):
  File "scipy/special/", line 404, in <module>
    import numpy
  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 30, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: cannot open shared object file: No such file or directory
Running scipy/special/
Running scipy/linalg/
Traceback (most recent call last):
  File "tools/", line 265, in <module>
  File "tools/", line 261, in main
  File "tools/", line 228, in find_process_files
    for result in pool.imap(lambda fn: process_generate_pyx(fn, lock), jobs):
  File "/usr/lib64/python2.7/multiprocessing/", line 673, in next
    raise value
RuntimeError: Running scipy/special/ failed
 * ERROR: sci-libs/scipy-1.0.0::gentoo failed (compile phase):
 *   (no error message)
 * Call stack:
 *, line  124:  Called src_compile
 *   environment, line 4207:  Called distutils-r1_src_compile
 *   environment, line 1265:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  371:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3653:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2794:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2792:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  836:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1258:  Called python_compile
 *   environment, line 3240:  Called die
 * The specific snippet of code:
 *       ${EPYTHON} tools/ || die;
 * If you need support, post the output of `emerge --info '=sci-libs/scipy-1.0.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-1.0.0::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-1.0.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-1.0.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0-python2_7'
 * S: '/var/tmp/portage/sci-libs/scipy-1.0.0/work/scipy-1.0.0'
Comment 1 Jonas Stein gentoo-dev 2018-01-13 18:30:38 UTC
Thank you for the report. Please recompile and *attach* the logfiles,
and reopen this ticket (Status:unconfirmed).
Comment 2 Andrew Ammerlaan gentoo-dev 2018-02-01 20:31:27 UTC
Created attachment 517488 [details]

I have the same problem, I went ahead and attached my build.log.
Comment 3 Andrew Ammerlaan gentoo-dev 2018-02-01 20:34:23 UTC
Created attachment 517490 [details]
Comment 4 Andrew Ammerlaan gentoo-dev 2018-02-01 20:35:20 UTC
Created attachment 517492 [details]
ebuild environment
Comment 5 Andrew Ammerlaan gentoo-dev 2018-02-24 10:05:06 UTC
I fixed this with:
emerge -1 blas-reference lapack-reference cblas-reference
eselect cblas set reference

cblas was previously set to gsl, idk if that was the cause of the issue or that just rebuilding blas and lapack would have been enough.
Comment 6 Kristian 2019-01-07 09:37:34 UTC
Rebuilding gsl (or whatever package is used for cblas; eselect cblas list) fixed this issue for me with gcc-8.2.0, scipy-1.1.0 and not being found while was provided by gcc.
Comment 7 Till Schäfer 2019-03-26 10:59:15 UTC
*** Bug 681786 has been marked as a duplicate of this bug. ***