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missing cparse.pyx file on the pypi ? #145

FrankFeng opened this Issue Feb 18, 2014 · 7 comments


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4 participants


When upgrading to pyvcf 0.6.6 via pip in Ubuntu, it failed with such an error:

error: can't copy 'vcf/cparse.pyx': doesn't exist or not a regular file

Then I download pyvcf 0.6.6 from pypi , uncompressed the file, and found there is no cparse.pyx .

So I manually downloaded the cparse.pyx file and put it into the vcf folder, and finally the setup could be finished. Hopefully I did it right here.

# download PyVCF 0.6.6 from pypi
wget https://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.6.6.tar.gz

tar -zxvf PyVCF-0.6.6.tar.gz

cd PyVCF-0.6.6/

# download cparse.pyx from github
wget -P ./vcf https://raw2.github.com/jamescasbon/PyVCF/master/vcf/cparse.pyx

# now run install
sudo python setup.py install


jamescasbon commented Feb 19, 2014

Duplicate of #69.

Generate the pyx file with cython.


jamescasbon commented Feb 20, 2014

My mistake, this is not a duplicate of #69. Apologies.

@jamescasbon jamescasbon reopened this Feb 20, 2014

This was referenced Feb 20, 2014


jamescasbon commented Feb 21, 2014

Can you try 0.6.7?

I tried pip install, and I could successfully installed pyvcf 0.6.7


jamescasbon commented Feb 21, 2014

No problem, enjoy!

dmb107 commented May 12, 2015

I apologize if this is a stupid question.

I receive the same "error: can't copy 'vcf/cparse.c': doesn't exist or not a regular file"
When I try to generate the pyx file with Cython, I get:

cython vcf/cparse.pyx
warning: vcf/cparse.pyx:16:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

I searched for that warning, but didn't find a good reply.


martijnvermaat commented May 12, 2015

@dmb107 How are you installing PyVCF? What is your environment (OS, Python version, are you using virtualenv)?

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