martijnvermaat
commented
12 years ago I assume python2.7 -c 'import pysam' is successful on your system?
Closed arq5x closed 12 years ago
martijnvermaat
commented
12 years ago I assume python2.7 -c 'import pysam' is successful on your system?
jamescasbon
commented
12 years ago 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 reply@reply.github.com wrote:
This is likely owing to my naivete, but I am working on another tool that depends upon PyVcf. As such, in my
setup.pyI 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
Reply to this email directly or view it on GitHub: https://github.com/jamescasbon/PyVCF/issues/32
James Casbon
Population Genetics - http://www.populationgenetics.com/ james.casbon@populationgenetics.com +44 (0)1223 497353
arq5x
commented
12 years ago 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
commented
12 years ago As an additional datapoint, I can replicate this with:
easy_install -U pyvcfwith 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
commented
12 years ago 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
commented
12 years ago @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.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 reply@reply.github.com wrote:
@jamescasbon it finds 0.4.1 just fine but I get the following error when running either
developorbuild. 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.
Reply to this email directly or view it on GitHub: https://github.com/jamescasbon/PyVCF/issues/32#issuecomment-4498071
James Casbon
Population Genetics - http://www.populationgenetics.com/ james.casbon@populationgenetics.com +44 (0)1223 497353
arq5x
commented
12 years ago Works like a charm! Thanks for working with me on this all.
No back to fixing a list of 20-odd bugs...
chapmanb
commented
12 years ago James; Awesome, thanks. 0.4.2 works cleanly for me.
This is likely owing to my naivete, but I am working on another tool that depends upon PyVcf. As such, in my
setup.pyI have: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?
The same error occurs with (upgrading from 0.4.0pre to 0.4.0):
The error: