Bug 622948 – dev-python/scipy-0.19.1 - from six.moves import urllib, map, filter ImportError: No module named moves

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description jorgicio 2017-06-28 18:55:29 UTC]

Scipy 0.19.0 was bumped, but this happens when I try to build it:

hackenherr:temp# emerge -1 scipy                                                                                                                               [13:58:50]
Calculating dependencies... done!

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) sci-libs/scipy-0.19.1::gentoo
 * scipy-0.19.1.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ...                                                                                                        [ ok ]
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
 * Using following Fortran compiler:
 *   F77: x86_64-pc-linux-gnu-gfortran
 *   FC:  x86_64-pc-linux-gnu-gfortran
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
>>> Unpacking source...
>>> Unpacking scipy-0.19.1.tar.gz to /var/tmp/portage/sci-libs/scipy-0.19.1/work
>>> Source unpacked in /var/tmp/portage/sci-libs/scipy-0.19.1/work
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
>>> Preparing source in /var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1 ...
 * Will copy sources from /var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1
 * python2_7: copying to /var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1-python2_7
 * python3_4: copying to /var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1-python3_4
>>> Source prepared.
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
>>> Configuring source in /var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1 ...
>>> Source configured.
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
>>> Compiling source in /var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1 ...
 * python2_7: running distutils-r1_run_phase python_compile
Traceback (most recent call last):
  File "/usr/lib/python-exec/python2.7/cython", line 6, in <module>
    from pkg_resources import load_entry_point
  File "/usr/lib64/python2.7/site-packages/pkg_resources/__init__.py", line 49, in <module>
    from six.moves import urllib, map, filter
ImportError: No module named moves
Processing scipy/linalg/cython_blas.pyx
Processing scipy/linalg/_solve_toeplitz.pyx
Processing scipy/linalg/_decomp_update.pyx.in
Processing scipy/linalg/cython_lapack.pyx
Processing scipy/signal/_spectral.pyx
Processing scipy/signal/_max_len_seq_inner.pyx
Processing scipy/signal/_upfirdn_apply.pyx
Processing scipy/interpolate/interpnd.pyx
Processing scipy/interpolate/_ppoly.pyx
Processing scipy/interpolate/_bspl.pyx
Processing scipy/io/matlab/mio_utils.pyx
Processing scipy/io/matlab/streams.pyx
Processing scipy/io/matlab/mio5_utils.pyx
Processing scipy/optimize/_group_columns.pyx
Processing scipy/optimize/_lsq/givens_elimination.pyx
Processing scipy/stats/_stats.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/_hierarchy.pyx
Processing scipy/special/_ellip_harm_2.pyx
Processing scipy/special/_comb.pyx
Processing scipy/special/_ufuncs_cxx.pyx
Processing scipy/special/_test_round.pyx
Processing scipy/special/cython_special.pyx
Processing scipy/special/_ufuncs.pyx
Processing scipy/_lib/_ccallback_c.pyx
Traceback (most recent call last):
  File "tools/cythonize.py", line 233, in <module>
    main()
  File "tools/cythonize.py", line 229, in main
    find_process_files(root_dir)
  File "tools/cythonize.py", line 220, in find_process_files
    process(cur_dir, fromfile, tofile, function, hash_db, pxi_hashes)
  File "tools/cythonize.py", line 190, in process
    processor_function(fromfile, tofile)
  File "tools/cythonize.py", line 71, in process_pyx
    raise Exception('Cython failed')
Exception: Cython failed
 * ERROR: sci-libs/scipy-0.19.1::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  115:  Called src_compile
 *   environment, line 4310:  Called distutils-r1_src_compile
 *   environment, line 1290:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  372:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3734:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2806:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2804:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  853:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1283:  Called python_compile
 *   environment, line 3321:  Called die
 * The specific snippet of code:
 *       ${EPYTHON} tools/cythonize.py || die;
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/scipy-0.19.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.19.1::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.19.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.19.1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1-python2_7'
 * S: '/var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1'
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
job-working-directory: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory

>>> Failed to emerge sci-libs/scipy-0.19.1, Log file:

>>>  '/var/tmp/portage/sci-libs/scipy-0.19.1/temp/build.log'

 * Messages for package sci-libs/scipy-0.19.1:

 * ERROR: sci-libs/scipy-0.19.1::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  115:  Called src_compile
 *   environment, line 4310:  Called distutils-r1_src_compile
 *   environment, line 1290:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  372:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3734:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2806:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2804:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  853:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1283:  Called python_compile
 *   environment, line 3321:  Called die
 * The specific snippet of code:
 *       ${EPYTHON} tools/cythonize.py || die;
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/scipy-0.19.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/scipy-0.19.1::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.19.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.19.1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1-python2_7'
 * S: '/var/tmp/portage/sci-libs/scipy-0.19.1/work/scipy-0.19.1'


Thanks in advance.

Tried with Python 2.7 and 3.4 and latest stable Cython.

Reproducible: Always

[Comment 1 jorgicio 2017-06-28 18:56:00 UTC]

Sorry, the version is 0.19.1.

[Comment 2 adebeus 2017-06-28 19:58:04 UTC]

I'm having the same problem.

[Comment 3 Jonas Stein 2017-06-28 20:36:31 UTC]

please sync again and retry with sci-libs/scipy-0.19.1
Does it work for you?

[Comment 4 jorgicio 2017-06-28 21:04:42 UTC]

Nop, the error is with 0.19.1, sorry, and resynced and still failing.

[Comment 5 François Bissey 2017-06-28 21:45:28 UTC]

You need to upgrade setuptools. I don't know the minimum version required but that did the trick for me.

[Comment 6 jorgicio 2017-06-28 21:50:03 UTC]

(In reply to François Bissey from comment #5)
> You need to upgrade setuptools. I don't know the minimum version required
> but that did the trick for me.

I'm using the latest stable one, the 34.0.2-r1 version (not the masked one), and the Scipy page doesn't show any information about minimum requirements.

[Comment 7 François Bissey 2017-06-28 21:59:06 UTC]

And scipy-0.19.1 is in unstable. So it is ok for it to depend on an unstable package. I couldn't find info on the minimum setuptools but because the failure occurred inside a setuptools file (/usr/lib64/python2.7/site-packages/pkg_resources/__init__.py) I thought it could be the culprit. I am now on setuptools-36.0.1. When I encountered the problem 12 hours ago, I didn't take the time to go through all the versions of setuptools in unstable to find the minimum one.

Note that 0.19.1 still exhibit the parallel build problem with python 3.6 described at https://bugs.gentoo.org/show_bug.cgi?id=614464

[Comment 8 adebeus 2017-06-29 03:48:38 UTC]

Upgrading to unstable setuptools fixed it for me - thanks!

[Comment 9 Sebastian Pucilowski 2017-06-29 09:13:48 UTC]

Confirming the same issue with scipy marked unstable, everything else normal.

  File "/usr/lib64/python2.7/site-packages/pkg_resources/__init__.py", line 49, in <module>
    from six.moves import urllib, map, filter
ImportError: No module named moves

[Comment 10 Roger 2019-11-11 21:48:51 UTC]

This error is still a problem with the latest stable =sci-libs/scipy-1.1.0.  Prior version build while the version 1.1.0 dies with the usual generic error, "${EPYTHON} tools/cythonize.py || die;"

Upgrading to "dev-python/setuptools-41.5.1" version still reproduces the same error with scipy.  (Required for net-wireless/gr-osmosdr package install.)

[Comment 11 Michał Górny 2021-02-24 20:51:06 UTC]

Closing bugs for old versions no longer in ::gentoo.  Please reopen if it still happens.