PyYaml dependency problems

[david4096]

When PyYAML can't install, it might fail quietly.

http://stackoverflow.com/questions/24791251/install-pyyaml-using-pip-add-pyyaml-as-pip-dependency

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----- Today January 9th, 2017 -----
[12:19 PM]
zfisch Hey David! I just updated the brcaexchange production site and saw a few warnings regarding GA4GH API dependencies. Could you check to make sure the API is working as intended?

Here’s what I saw in the terminal when installing requirements:

  Running setup.py install for PyYAML
    checking if libyaml is compilable
    x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c build/temp.linux-x86_64-2.7/check_libyaml.c -o build/temp.linux-x86_64-2.7/check_libyaml.o
    build/temp.linux-x86_64-2.7/check_libyaml.c:2:18: fatal error: yaml.h: No such file or directory
     #include <yaml.h>
                      ^
    compilation terminated.

    libyaml is not found or a compiler error: forcing --without-libyaml
    (if libyaml is installed correctly, you may need to
     specify the option --include-dirs or uncomment and
     modify the parameter include_dirs in setup.cfg)

  Could not find .egg-info directory in install record for PyYAML==3.12
  Running setup.py install for ga4gh-common

    Skipping installation of /var/www/backend/production/virtualenv/lib/python2.7/site-packages/ga4gh/__init__.py (namespace package)
    Installing /var/www/backend/production/virtualenv/lib/python2.7/site-packages/ga4gh_common-0.0.5-py2.7-nspkg.pth
    Installing ga4gh_run_tests script to /var/www/backend/production/virtualenv/bin
  Could not find .egg-info directory in install record for ga4gh-common==0.0.5
  Running setup.py install for ga4gh-schemas

    Skipping installation of /var/www/backend/production/virtualenv/lib/python2.7/site-packages/ga4gh/__init__.py (namespace package)
    Installing /var/www/backend/production/virtualenv/lib/python2.7/site-packages/ga4gh_schemas-0.0.8-py2.7-nspkg.pth
  Could not find .egg-info directory in install record for ga4gh-schemas==0.0.8
Successfully installed PyYAML ga4gh-common ga4gh-schemas
Cleaning up…```

[dcolligan]

@david4096 couple questions: 1) is this filed in the correct place? other projects of ours also use yaml and 2) what can be done about this? add info to the docs? conda?

[david4096]

I think this is only used for doing test harness stuff to run travis tests locally. There is probably a better supported package, because in the server there are two yaml packages in dev-requirements, which I think we can treat as a separate issue. https://github.com/ga4gh/server/blob/master/dev-requirements.txt

I posted this issue when helping with an install of the schemas for the BRCA Exchange API. The install succeeded even though PyYAML failed to install properly, the result being unable to run the test harness, no big deal. This is a silent error that doesn't hurt much, but I wanted to post it here.

[dcolligan]

Is this a WONTFIX then?