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Error on install using pip (v0.6.6) #147

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lemieuxl opened this Issue · 1 comment

2 participants

@lemieuxl

The following error occured while installing PyVCF version 0.6.6 using pip on a python virtual environment. In brief, it seems that the file vcf/cparse.pyx is absent from the archive (even when downloaded from PyPI).

$ pip install -U PyVCF
Downloading/unpacking PyVCF
  Downloading PyVCF-0.6.6.tar.gz
  Running setup.py (path:/home/user/softwares/Python-2.7.6_virtualenv/build/PyVCF/setup.py) egg_info for package PyVCF

Requirement already up-to-date: distribute in /home/user/softwares/Python-2.7.6_virtualenv/lib/python2.7/site-packages (from PyVCF)
Requirement already up-to-date: setuptools>=0.7 in /home/user/softwares/Python-2.7.6_virtualenv/lib/python2.7/site-packages (from distribute->PyVCF)
Installing collected packages: PyVCF
  Running setup.py install for PyVCF

    error: can't copy 'vcf/cparse.pyx': doesn't exist or not a regular file
    Complete output from command /home/user/softwares/Python-2.7.6_virtualenv/bin/python -c "import setuptools, tokenize;__file__='/home/user/softwares/Python-2.7.6_virtualenv/build/PyVCF/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-F4PiFh-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/user/softwares/Python-2.7.6_virtualenv/include/site/python2.7:
    running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.7

creating build/lib.linux-x86_64-2.7/vcf

copying vcf/__init__.py -> build/lib.linux-x86_64-2.7/vcf

copying vcf/filters.py -> build/lib.linux-x86_64-2.7/vcf

copying vcf/utils.py -> build/lib.linux-x86_64-2.7/vcf

copying vcf/parser.py -> build/lib.linux-x86_64-2.7/vcf

copying vcf/model.py -> build/lib.linux-x86_64-2.7/vcf

creating build/lib.linux-x86_64-2.7/vcf/test

copying vcf/test/__init__.py -> build/lib.linux-x86_64-2.7/vcf/test

copying vcf/test/prof.py -> build/lib.linux-x86_64-2.7/vcf/test

copying vcf/test/test_vcf.py -> build/lib.linux-x86_64-2.7/vcf/test

running egg_info

writing dependency_links to PyVCF.egg-info/dependency_links.txt

writing requirements to PyVCF.egg-info/requires.txt

writing PyVCF.egg-info/PKG-INFO

writing top-level names to PyVCF.egg-info/top_level.txt

writing entry points to PyVCF.egg-info/entry_points.txt

warning: manifest_maker: standard file '-c' not found



reading manifest file 'PyVCF.egg-info/SOURCES.txt'

writing manifest file 'PyVCF.egg-info/SOURCES.txt'

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

----------------------------------------
Cleaning up...
Command /home/user/softwares/Python-2.7.6_virtualenv/bin/python -c "import setuptools, tokenize;__file__='/home/user/softwares/Python-2.7.6_virtualenv/build/PyVCF/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-F4PiFh-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/user/softwares/Python-2.7.6_virtualenv/include/site/python2.7 failed with error code 1 in /home/user/softwares/Python-2.7.6_virtualenv/build/PyVCF
Storing debug log for failure in /home/user/.pip/pip.log
@jamescasbon
Owner

Thanks, I'm going to close this in favour of #145. I will check it out when I get a minute.

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