Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix travis build failing due to missing libgfortran.1 lib #17

Closed
orbeckst opened this issue Sep 22, 2015 · 5 comments
Closed

fix travis build failing due to missing libgfortran.1 lib #17

orbeckst opened this issue Sep 22, 2015 · 5 comments
Assignees
@orbeckst
Labels
testing
Milestone
0.3

Comments

@orbeckst
Copy link
Member

The 2.7 travis build fails with

Failure: ImportError (libgfortran.so.1: cannot open shared object file: No such file or directory) ... ERROR

The problem is described in travis-ci/travis-ci#4816 and I am trying to fix it in the same manner: by using a newer version of scipy in conda:

conda install --yes numpy=1.9.1 scipy=0.16
@orbeckst orbeckst self-assigned this Sep 22, 2015
orbeckst added a commit that referenced this issue Sep 22, 2015
@orbeckst
fix failing Travis-CI build due to missing libgfortran #17
6ff73b6
@orbeckst
Copy link
Member Author

That did not help... https://travis-ci.org/MDAnalysis/GridDataFormats/jobs/81666101 failed.

orbeckst added a commit that referenced this issue Sep 22, 2015
@orbeckst
try to provide libgfortran.so.1 through package libgfortran3 #17
3eec913
@orbeckst
Copy link
Member Author

@richardjgowers , any idea how to fix this problem? The issue/17 branch is currently failing but only for 2.7. This seems an issue with the conda scipy package but I have zero clue how to fix it.
I'll make the branch a PR just to make it more visible.

@orbeckst orbeckst mentioned this issue Sep 22, 2015
Merged
@orbeckst orbeckst added this to the 0.3 milestone Sep 22, 2015
@orbeckst
Copy link
Member Author

Blocks the 0.3.0 release because I don't want to have a "failing" badge associate with the release... even though it seems to be a travis/conda problem.

@orbeckst
Copy link
Member Author

This is a problem with conda/conda#444 and they only updated numpy 1.9.2 (our travis runs on 1.9.1) so I'll try to upgrade...

orbeckst added a commit that referenced this issue Sep 22, 2015
@orbeckst
upgrade travis to numpy 1.9.2 to get fixed conda package
1a0d676 
Should fix #17.

See conda/conda#444 (which was only fixed for 1.5.1, 1.6.2, 1.7.1, 1.8.2, 1.9.2).
@orbeckst
Copy link
Member Author

Trying a workaround to use conda scipy package without MKL because @bartvm in mila-iqia/blocks#836 suggests to disable MKL in numpy 1.9.2 because the MKL version is still missing the libgfortran.so.1 dependency.

orbeckst added a commit that referenced this issue Sep 23, 2015
@orbeckst
fix failing Travis-CI build due to missing libgfortran #17
41b8d96 
- noted on  travis-ci/travis-ci#4816 and identified as a problem with conda
  packages numpy and scipy for Python 2.7 (see conda/conda#444)
- need to use numpy 1.9.2 without MKL
  - conda/conda#444 (which was only fixed for 1.5.1, 1.6.2, 1.7.1, 1.8.2, 1.9.2)
  - See mila-iqia/blocks#836 : @bartvm suggests to disable MKL in numpy 1.9.2
    because the MKL version is still missing the libgfortran.so.1 dependency.
- also updated scipy to 0.16.0
@orbeckst orbeckst mentioned this issue Oct 6, 2015
Merged
@tylerjereddy tylerjereddy mentioned this issue Oct 22, 2015
Merged
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Nov 5, 2015
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
e0eb6e3 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Dec 1, 2015
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
941bcb3 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Dec 3, 2015
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
dfae55c 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Dec 7, 2015
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
7e37900 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Dec 8, 2015
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
51eaa21 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
@orbeckst orbeckst mentioned this issue Dec 10, 2015
Closed
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Dec 22, 2015
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
8c1cb08 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
tylerjereddy added a commit to MDAnalysis/mdanalysis that referenced this issue Jan 5, 2016
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
279712f 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
orbeckst pushed a commit to MDAnalysis/mdanalysis that referenced this issue Jan 29, 2016
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
a4f0469 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
orbeckst pushed a commit to MDAnalysis/mdanalysis that referenced this issue Jul 6, 2016
@tylerjereddy @orbeckst
adjusted travis configuration (without netcdflib)
a61df8b 
- removed netCDF4 and dependencies from travis configuration
- fix scipy.io import problem relating to libgfortran Travis CI problem
  described in Issue MDAnalysis/GridDataFormats#17.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@orbeckst orbeckst

Labels
testing
Projects
None yet
Milestone
0.3
Development

No branches or pull requests
1 participant
@orbeckst