htseq: error: too many arguments to function

[sjackman]

    pysam/libchtslib.c: In function '__Pyx_PyCFunction_FastCall':
    pysam/libchtslib.c:15077:12: error: too many arguments to function '(PyObject * (*)(PyObject *, PyObject * const*, Py_ssize_t))meth'
         return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);

https://hub.docker.com/r/bcgsc/orca-1/builds/brdtjmj5vdtd9ifucknylnu/

@suujia Can you see if you can find any reference to this error on the upstream GitHub repo?
https://github.com/simon-anders/htseq

[sjackman]

This may be caused by the upgrade from Python 3.6 to Python 3.7.

[sjackman]

I've removed htseq with PR #61. Still be worth looking into the build failure, but not a priority.

[sjackman]

pip3 install biopython is failing as well, and we can't remove biopython from ORCA. pip2 install biopython did however succeed.
https://hub.docker.com/r/bcgsc/orca-1/builds/bwhqkj3gdt2w8rwhrmmbhug/

Could you please look into this build failure?

[suujia]

a potential alternative:

# Install Numpy and Scipy
RUN apt-get build-dep --yes python-biopython

# Install BioPython
RUN apt-get install --yes \
 python-biopython=1.63-1 \
 python-biopython-sql=1.63-1

[suujia]

Oh so the brew formula for python changed 9 days ago to version 3.70
Here's a couple issues associating Biopython with python 3.70: pypa/pip#5250

Regarding this error message: Cache entry deserialization failed, entry ignored (found in pypa/pip#5250)

I suspect that the problem is that cache entries created in Python 2 cannot be deserialized
in Python 3. If I use the --cache-dir option to force different caches for Python 2 and 
Python 3, the problem goes away.

[suujia]

This issue from pip3 install seem to be fixed from below two lines:

Command "python setup.py egg_info" failed with error code 1 

here

apt-get install libmysqlclient-dev

here
and here

pip install --upgrade setuptools 

[suujia]

pip3 install --upgrade setuptools fixes:

failed with error code 1 in /tmp/pip-install-n9KU9C/python-igraph/
&& 
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-5jyce1_7/ruamel.yaml/

[sjackman]

Nice find!

[suujia]

Hi Just to clarify, htseq is removed currently. We have python3.7 however, it says that htseq is only tested up to python3.6. However I have tested pip2 install htseq and it works perfectly. Would that be a good enough alternative?
simon-anders/htseq#60