Pysam builds failing on TravisCI

[jeromekelleher]

Since 0.8.2 was released, Pysam builds seem to fail on TravisCI. See

https://travis-ci.org/ga4gh/server/builds/51162225

for example. We get gcc: error: pysam/csamtools.c: No such file or directory and compilation fails.

[AndreasHeger]

Thanks. It seems that csamtools.c was not added to the tar-ball, I am
not sure why.

I will release a fixed version later today.

Best wishes,
Andreas

On 02/18/15 10:18, Jerome Kelleher wrote:

Since 0.8.2 was released, Pysam builds seem to fail on TravisCI. See

https://travis-ci.org/ga4gh/server/builds/51162225

for example. We get |gcc: error: pysam/csamtools.c: No such file or
directory| and compilation fails.

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[AndreasHeger]

Can you please try again? 0.8.2.1 seems to install cleanly via pip.

Best wishes,
Andreas

[jeromekelleher]

This works now; thanks @AndreasHeger!

[jeromekelleher]

Closing this issue as our Travis builds are now working. Thanks for the quick fix @AndreasHeger.

[JCSzamosi]

I am having this issue on Ubuntu with 0.8.4. The same file was missing when I downloaded the tarball.

I tried cloning the repository and now a different file is missing:

x86_64-linux-gnu-gcc: error: pysam/chtslib.c: No such file or directory

[AndreasHeger]

Thanks, @JCSzamosi i, do you have cython installed? The .c files are not part of the repository. Best wishes, Andreas

[JCSzamosi]

Hi Andreas,

Yes I do have cython installed. From the man page it looks like I have
version 0.20.1post0

On Sat, Feb 6, 2016 at 3:00 PM, Andreas Heger notifications@github.com
wrote:

Thanks, @JCSzamosi https://github.com/JCSzamosi i, do you have cython
installed? The .c files are not part of the repository. Best wishes, Andreas

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J. C. Szamosi, M.Sc.
Bioinformatician
Farncombe Metagenomics Facility
McMaster University