PyPI 0.4.0 installation issues via setuptools about pyvcf

[martijnvermaat]

I assume python2.7 -c 'import pysam' is successful on your system?

[jamescasbon]

Ooh, sorry about that!

What happens if you 'pip install pyvcf'? Do you get the same error?

The only obvious thing is that I do a try/import
pysam/except/pysam=None. If pysam is in some semi installed state,
this could cause problems.

Can you try installing pysam and then rerunning python setup.py
develop/install. I would guess that would be a workaround.

Given the mess that is python packaging, a 'python setup install'
could be doing several things. Which setup function are you importing
and running?

On Wed, Mar 14, 2012 at 2:31 AM, Aaron Quinlan
[email protected]
wrote:

This is likely owing to my naivete, but I am working on another tool that depends upon PyVcf.  As such, in my setup.py I have:

   install_requires=['numpy', 'pyparsing', 'pysam', 'pyvcf>=0.4.0'],

When running setup.py develop/install, this causes the script to search PyPI for the latest version of PyPI.  It succeeds in finding it, but when trying to install it, I get the following error.  I am really, really new to setuptools, so I don't have many ideas here, but it looks like there is a problem compiling the pysam or tabix Extension module.  Any ideas?

   Processing dependencies for pop==0.1.0
   Searching for pyvcf>=0.4.0
   Reading http://pypi.python.org/simple/pyvcf/
   Reading https://github.com/jamescasbon/PyVCF
   Best match: PyVCF 0.4.0
   Downloading http://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.4.0.tar.gz#md5=165224e91a38f5a6c0fa3d63b8258b58
   Processing PyVCF-0.4.0.tar.gz
   Running PyVCF-0.4.0/setup.py -q bdist_egg --dist-dir /var/folders/tO/tOq24FDAF-WH1NXQLRXlhk+++TM/-Tmp-/easy_install-kE7hJH/PyVCF-0.4.0/egg-dist-tmp-1zQvoE
   Traceback (most recent call last):
     File "setup.py", line 45, in
       'Topic :: Scientific/Engineering :: Bio-Informatics']
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 152, in setup
       dist.run_commands()
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
       self.run_command(cmd)
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
       cmd_obj.run()
     File "build/bdist.linux-i686/egg/setuptools/command/develop.py", line 27, in run
     File "build/bdist.linux-i686/egg/setuptools/command/develop.py", line 102, in install_for_development
     File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 519, in process_distribution
     File "build/bdist.linux-i686/egg/pkg_resources.py", line 563, in resolve
     File "build/bdist.linux-i686/egg/pkg_resources.py", line 799, in best_match
     File "build/bdist.linux-i686/egg/pkg_resources.py", line 811, in obtain
     File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 446, in easy_install
     File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 476, in install_item
     File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 655, in install_eggs
     File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 930, in build_and_install
     File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 919, in run_setup
     File "build/bdist.linux-i686/egg/setuptools/sandbox.py", line 62, in run_setup
     File "build/bdist.linux-i686/egg/setuptools/sandbox.py", line 105, in run
     File "build/bdist.linux-i686/egg/setuptools/sandbox.py", line 64, in
     File "setup.py", line 12, in
       m.Extension.dict = m._Extension.dict
     File "/var/folders/tO/tOq24FDAF-WH1NXQLRXlhk+++TM/-Tmp-/easy_install-kE7hJH/PyVCF-0.4.0/vcf/init.py", line 166, in
     File "/var/folders/tO/tOq24FDAF-WH1NXQLRXlhk+++TM/-Tmp-/easy_install-kE7hJH/PyVCF-0.4.0/vcf/parser.py", line 10, in
     File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysam-0.6-py2.7-macosx-10.6-intel.egg/pysam/init.py", line 1, in
       from csamtools import *
     File "csamtools.pxd", line 60, in init csamtools (pysam/csamtools.c:32571)
   TypeError: builtin.file is not a type object

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#32

James Casbon

Population Genetics - http://www.populationgenetics.com/
[email protected]
[phone]

[arq5x]

I already have pysam installed, so:

@martijnvermaat python2.7 -c 'import pysam' is successful, yes.

@jamescasbon yes, pip install --upgrade pyvcf works.

@jamescasbon I am new to this so I am just learning how messy this is. Here is my setup.py:
https://gist.github.com/2035775

Thanks for the help all!t

[chapmanb]

As an additional datapoint, I can replicate this with:

easy_install -U pyvcf

with pysam-0.6 installed on Ubuntu 11.10. pip does work cleanly.

The Biopython setup avoids doing an import to get the version, presumably for this reason, and just parses it out:

https://github.com/biopython/biopython/blob/master/setup.py#L397

[jamescasbon]

Thanks, @chapmanb for the tip.

I just released 0.4.1 on pypi which avoids import during setup. Can you good people try installing that and see if it is fixed?

[arq5x]

@jamescasbon it finds 0.4.1 just fine but I get the following error when running either develop or build. This might this be specific to me...

Searching for pyvcf>=0.4.1
Reading http://pypi.python.org/simple/pyvcf/
Reading https://github.com/jamescasbon/PyVCF
Best match: PyVCF 0.4.1
Downloading http://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.4.1.tar.gz#md5=48cb5f4c9821d7e573f0377ae5d1c7b2
Processing PyVCF-0.4.1.tar.gz
Running PyVCF-0.4.1/setup.py -q bdist_egg --dist-dir /var/folders/tO/tOq24FDAF-WH1NXQLRXlhk+++TM/-Tmp-/easy_install-2BBNI6/PyVCF-0.4.1/egg-dist-tmp-nrk278
error: SandboxViolation: file('/tmp/ds', 'w') {}

The package setup script has attempted to modify files on your system
that are not within the EasyInstall build area, and has been aborted.

This package cannot be safely installed by EasyInstall, and may not
support alternate installation locations even if you run its setup
script by hand.  Please inform the package's author and the EasyInstall
maintainers to find out if a fix or workaround is available.

[jamescasbon]

I'm an idiot and left in debugging statement 0.4.2 should fix that,
just released.

Apologies all for doing this via releases, I couldn't replicate the
problem here.

On Wed, Mar 14, 2012 at 1:35 PM, Aaron Quinlan
[email protected]
wrote:

@jamescasbon it finds 0.4.1 just fine but I get the following error when running either develop or build.  This might this be specific to me...

   Searching for pyvcf>=0.4.1
   Reading http://pypi.python.org/simple/pyvcf/
   Reading https://github.com/jamescasbon/PyVCF
   Best match: PyVCF 0.4.1
   Downloading http://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.4.1.tar.gz#md5=48cb5f4c9821d7e573f0377ae5d1c7b2
   Processing PyVCF-0.4.1.tar.gz
   Running PyVCF-0.4.1/setup.py -q bdist_egg --dist-dir /var/folders/tO/tOq24FDAF-WH1NXQLRXlhk+++TM/-Tmp-/easy_install-2BBNI6/PyVCF-0.4.1/egg-dist-tmp-nrk278
   error: SandboxViolation: file('/tmp/ds', 'w') {}

   The package setup script has attempted to modify files on your system
   that are not within the EasyInstall build area, and has been aborted.

   This package cannot be safely installed by EasyInstall, and may not
   support alternate installation locations even if you run its setup
   script by hand.  Please inform the package's author and the EasyInstall
   maintainers to find out if a fix or workaround is available.

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Reply to this email directly or view it on GitHub:
#32 (comment)

James Casbon

Population Genetics - http://www.populationgenetics.com/
[email protected]
[phone]

[arq5x]

Works like a charm! Thanks for working with me on this all.

No back to fixing a list of 20-odd bugs...

[chapmanb]

James;
Awesome, thanks. 0.4.2 works cleanly for me.