compilation error after lastest pull

[IanSudbery]

Hi,

When trying to update extensions after the latest pull, I get the following error:

cythoning scripts/_bam2stats.pyx to scripts/_bam2stats.c

Error compiling Cython file:
------------------------------------------------------------
...
    cdef int x
    cdef int lflags = len(FLAGS)
    cdef int f

    # detailed counting
    cdef PersistentFastqProxy fq
        ^
------------------------------------------------------------

scripts/_bam2stats.pyx:91:9: 'PersistentFastqProxy' is not a type identifier
building 'CGAT._bam2stats' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/home/mb1ims/.conda/envs/mb1ims/lib/python2.7/site-packages/numpy/core/include -I/home/mb1ims/.conda/envs/mb1ims/lib/python2.7/site-packages/pysam -I/home/mb1ims/.conda/envs/mb1ims/lib/python2.7/site-packages/pysam/include/htslib -I/home/mb1ims/.conda/envs/mb1ims/lib/python2.7/site-packages/pysam/include/samtools -I/home/mb1ims/.conda/envs/mb1ims/include/python2.7 -c scripts/_bam2stats.c -o build/temp.linux-x86_64-2.7/scripts/_bam2stats.o
scripts/_bam2stats.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
error: command 'gcc' failed with exit status 1

I think this looks like a pysam error.
pysam is version 0.8.3 via the cgat conda channel.

Cheers,

Ian

[sebastian-luna-valero]

Hi Ian,

Try adding the bioconda channel and updating your conda installation:

conda config --add channels https://conda.anaconda.org/bioconda
conda update --all

Best regards,
Sebastian

[IanSudbery]

Thanks sebastian. Should I be using bioconda instead of cgat? Is all the cgat stuff now in bioconda? I noicte when I do this that I'm getting cgat's r-lite rather than r from bioconda for example.

[sebastian-luna-valero]

Hi Ian,

Thanks for your feedback.

Please use both of them. I have to think about how to split conda packages between those repositories.

Regarding R, I am now using the R specific channel as well:
https://conda.anaconda.org/r

and that is where future CGAT packages will be pointing to.

Best regards,
Sebastian.

[IanSudbery]

Hi @sebastian-luna-valero ,

I thought you might like to know that doing a conda update --all updates bx-python. This bx-python update requires a new numpy version, but for some reason, this isn't installed. You get this error when you build the cgat extensions:

File "/home/travis/build/CGATOxford/cgat/scripts/gtf2table.py", line 483, in <module>
    import bx.bbi.bigwig_file
  File "bx/bbi/bigwig_file.pyx", line 1, in init bx.bbi.bigwig_file (lib/bx/bbi/bigwig_file.c:7691)
  File "__init__.pxd", line 155, in init bx.bbi.bbi_file (lib/bx/bbi/bbi_file.c:12824)
ValueError: numpy.dtype has the wrong size, try recompiling

You get this from any script that uses bx.

If you uninstall bx-python and reinstall it, the new version of numpy is installed.

I'm letting you know this, mostly because this is the reason your build on Travis is currently failing.

Ian

[sebastian-luna-valero]

Hi Ian,

Thank you very much. I was working on this earlier this week but got distracted with other important issues.

You are certainly right. I had to update the ggplot package which was built with numpy 1.9 and that was causing the problem. The tests passed locally and I am now rebuilding on Travis to check.

Best regards,
Sebastian.

[sebastian-luna-valero]

Thanks again, that fixed it.

Best regards,
Sebastian.