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cgat-developers / cgat-flow

cgat-flow repository
MIT License
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updated Rmarkdown report so tests pass and it runs to completion with… #96

Closed Acribbs closed 5 years ago

Acribbs commented 5 years ago

… all plots generated

Acribbs commented 5 years ago

The conda update is because I was seeing hated object errors that have been fixed in Linux, now I’m seeing other errors in OS X build.

Please advise if you had any suggestions.

sebastian-luna-valero commented 5 years ago

Tricky one.

The last error I am getting is:

ImportError: /home/travis/cgat-install/cgat-apps/cgat/BamTools/bamtools.cpython-36m-x86_64-linux-gnu.so: undefined symbol: bam_read1

But pysam and co. are all the same between OSX (tests passing) and Linux (failing).

Will have a look next week.

Any suggesions?

Best regards, Sebastian

Acribbs commented 5 years ago

Hi @sebastian-luna-valero, from my local testing of cgat-apps in python 3.7 environment I am getting problems with running anything that contains cython code. For example

 cgat bam2bed --help
Traceback (most recent call last):
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/py37-test/bin/cgat", line 11, in <module>
    sys.exit(main())
  File "/ifs/devel/adamc/cgat-developers/cgat-apps/cgat/cgat.py", line 129, in main
    module = imp.load_module(command, file, pathname, description)
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/py37-test/lib/python3.7/imp.py", line 234, in load_module
    return load_source(name, filename, file)
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/py37-test/lib/python3.7/imp.py", line 171, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 696, in _load
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/ifs/devel/adamc/cgat-developers/cgat-apps/cgat/tools/bam2bed.py", line 113, in <module>
    from cgat.BamTools.bamtools import merge_pairs
ModuleNotFoundError: No module named 'cgat.BamTools.bamtools'

Could there be an issue with the latest packaging of the cgat-apps in bioconda?

I see in the recipe you modified the cython version

Acribbs commented 5 years ago

Hmm, looks like the latest python 3.6 version of cgat-apps is also broken, but slightly different error:

cgat bam2bed --help
Traceback (most recent call last):
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/py36-test/bin/cgat", line 11, in <module>
    sys.exit(main())
  File "/ifs/devel/adamc/cgat-developers/cgat-apps/cgat/cgat.py", line 129, in main
    module = imp.load_module(command, file, pathname, description)
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/py36-test/lib/python3.6/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/py36-test/lib/python3.6/imp.py", line 172, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 684, in _load
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/ifs/devel/adamc/cgat-developers/cgat-apps/cgat/tools/bam2bed.py", line 113, in <module>
    from cgat.BamTools.bamtools import merge_pairs
  File "cgat/BamTools/bamtools.pyx", line 21, in init cgat.BamTools.bamtools
ModuleNotFoundError: No module named 'sortedcontainers'
Acribbs commented 5 years ago

@sebastian-luna-valero after testing OSX and Linux versions of cgat-apps, it seems like cgat-apps works fine for both python 3.6 and 3.7. However, for linux the version only python 3.6 and not python 3.7 works. This may be why or testing is breaking for cgat-flow for linux?