Travis build failing - libgfortran related?

choderalab / assaytools

Modeling and Bayesian analysis of fluorescence and absorbance assays.

http://assaytools.readthedocs.org

GNU Lesser General Public License v2.1

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Travis build failing - libgfortran related? #119

Closed sonyahanson closed 7 years ago

sonyahanson commented 7 years ago

Seems like the travis build is currently failing, potentially because of this line in our conda recipe: - libgfortran ==1.0.0 [linux]

This is the commit that changed this: https://github.com/choderalab/assaytools/commit/8e6f35eb7bbcf237386248f054a46b2fed1cc90a

Seems like we are no longer pinning the pymc version. Do we have to keep this libgfortran version pinned for some other reason?

bas-rustenburg commented 7 years ago

The commit you point to pins pymc, and gfortran.

This one unpins only pymc. Has it been broken for that long,, or did something else change too?

https://github.com/choderalab/assaytools/commit/7adbe6e0deb191cf88aaaebd8aa500fc1d93fc61#diff-23fca1736cbf667a8319e570051bbe20

MehtapIsik commented 7 years ago

This problem looks similar to assaytools installation problems I have been having, because of pymc dependency. The combination of versions that worked for me in the end is:

pymc                      2.3.6 
libgfortran               3.0.0  
gcc                       4.8.5 
libgcc                    5.2.0

sonyahanson commented 7 years ago

I wonder if @jchodera noticed if this was happening when he cut a release in June: https://github.com/choderalab/assaytools/pull/111

bas-rustenburg commented 7 years ago

It looks like that PR might have been merged before the travis tests had a chance to run, which would lead to the travis logs you see there.

jchodera commented 7 years ago

Looks like this is because libgfortran 1.0 has been removed from standard channels. Now that we're requiring conda-forge, we need to:

Add conda-forge to the channels in .travis.yaml according to these instructions:
```
conda config --add channels omnia --add channels conda-forge
```
This should cause pymc to be picked up from conda-forge
Remove the libgfortran explicit dependency in devtools/conda-recipe/meta.yaml, since I don't think this should be explicitly specified anymore; we should rely on the conda-forge pymc to include its own dependencies.