PyVCF
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jamescasbon
Error on install
Hi,
when I try to install PyVCF 0.6.0 through python setup.py install on a mac I get the following:
error: can't copy 'vcf/cparse.c': doesn't exist or not a regular file
The file ins't in the vcf directory. Am I doing something wrong? Did I miss a step?
thanks
jm
Can you let me know your python version?
Can you try installing cython?
python is: Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
I did install cython (Cython version 0.16)
I have to say that I am a newb at this, so it is very much likely that I'm doing something wrong...
On Wed, Aug 22, 2012 at 3:21 PM, James Casbon [email protected]:
Can you let me know your python version?
Can you try installing cython?
— Reply to this email directly or view it on GitHubhttps://github.com/jamescasbon/PyVCF/issues/69#issuecomment-7935666.
Can you paste the entire output of python setup.py install, please? And the output of tree, if possible
output of install is:
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'use_2to3' warnings.warn(msg) running install running bdist_egg running egg_info 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 dependency_links to PyVCF.egg-info/dependency_links.txt writing entry points to PyVCF.egg-info/entry_points.txt reading manifest file 'PyVCF.egg-info/SOURCES.txt' writing manifest file 'PyVCF.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-10.6-universal/egg running install_lib running build_py error: can't copy 'vcf/cparse.c': doesn't exist or not a regular file
I have never used tree before and I don't think I have it installed.. happy to install it if you let me know where to find it for mac.
On Wed, Aug 22, 2012 at 3:43 PM, James Casbon [email protected]:
Can you paste the entire output of python setup.py install, please? And the output of tree, if possible
— Reply to this email directly or view it on GitHubhttps://github.com/jamescasbon/PyVCF/issues/69#issuecomment-7936421.
this may be helpful, though (ls -r * in PyVCF's directory):
LICENSE README.rst setup.py tox.ini
PyVCF.egg-info: PKG-INFO dependency_links.txt requires.txt SOURCES.txt entry_points.txt top_level.txt
build: lib.macosx-10.6-universal-2.6 temp.macosx-10.6-universal-2.6
build/lib.macosx-10.6-universal-2.6: vcf
build/lib.macosx-10.6-universal-2.6/vcf: init.py filters.py parser.py utils.py cparse.c model.py test
build/lib.macosx-10.6-universal-2.6/vcf/test: 1kg.vcf.gz example-4.1-sv.vcf issue_49.vcf tb.vcf.gz.tbi init.py example-4.1.vcf null_genotype_mono.vcf test_vcf.py bcftools.vcf freebayes.vcf prof.py walk_left.vcf example-4.0.vcf gatk.vcf samtools.vcf example-4.1-bnd.vcf issue-16.vcf tb.vcf.gz
build/temp.macosx-10.6-universal-2.6: vcf
build/temp.macosx-10.6-universal-2.6/vcf:
docs: API.rst HISTORY.rst Makefile index.rst FILTERS.rst INTRO.rst conf.py
scripts: vcf_filter.py vcf_melt
vcf: init.py filters.py parser.py utils.py cparse.pyx model.py test
vcf/test: 1kg.vcf.gz example-4.1-bnd.vcf issue-16.vcf tb.vcf.gz README.md example-4.1-sv.vcf issue_49.vcf tb.vcf.gz.tbi init.py example-4.1.vcf null_genotype_mono.vcf test_vcf.py bcftools.vcf freebayes.vcf prof.py walk_left.vcf example-4.0.vcf gatk.vcf samtools.vcf
On Wed, Aug 22, 2012 at 4:54 PM, Jose Bras [email protected] wrote:
output of install is:
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'use_2to3' warnings.warn(msg) running install running bdist_egg running egg_info 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 dependency_links to PyVCF.egg-info/dependency_links.txt writing entry points to PyVCF.egg-info/entry_points.txt reading manifest file 'PyVCF.egg-info/SOURCES.txt' writing manifest file 'PyVCF.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-10.6-universal/egg running install_lib running build_py error: can't copy 'vcf/cparse.c': doesn't exist or not a regular file
I have never used tree before and I don't think I have it installed.. happy to install it if you let me know where to find it for mac.
On Wed, Aug 22, 2012 at 3:43 PM, James Casbon [email protected]:
Can you paste the entire output of python setup.py install, please? And the output of tree, if possible
— Reply to this email directly or view it on GitHubhttps://github.com/jamescasbon/PyVCF/issues/69#issuecomment-7936421.
Can you try runing cython on vcf/cparse.pyx?
This should generate vcf/cparse.c and then the build will happen.
Perhaps I should just check in that file. I can't understand why it is not being built. Apologies!
ok - no errors on install. but when I import this in python it tells me that the module is not installed... I'm pasting the install output below. I don't see any errors. Did I miss something?
Great thanks for helping me out with this.
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'use_2to3' warnings.warn(msg) running install running bdist_egg running egg_info 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 dependency_links to PyVCF.egg-info/dependency_links.txt writing entry points to PyVCF.egg-info/entry_points.txt reading manifest file 'PyVCF.egg-info/SOURCES.txt' writing manifest file 'PyVCF.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-10.6-universal/egg running install_lib running build_py running build_ext creating build/bdist.macosx-10.6-universal/egg creating build/bdist.macosx-10.6-universal/egg/vcf copying build/lib.macosx-10.6-universal-2.6/vcf/init.py -> build/bdist.macosx-10.6-universal/egg/vcf copying build/lib.macosx-10.6-universal-2.6/vcf/cparse.c -> build/bdist.macosx-10.6-universal/egg/vcf copying build/lib.macosx-10.6-universal-2.6/vcf/cparse.so -> build/bdist.macosx-10.6-universal/egg/vcf copying build/lib.macosx-10.6-universal-2.6/vcf/filters.py -> build/bdist.macosx-10.6-universal/egg/vcf copying build/lib.macosx-10.6-universal-2.6/vcf/model.py -> build/bdist.macosx-10.6-universal/egg/vcf copying build/lib.macosx-10.6-universal-2.6/vcf/parser.py -> build/bdist.macosx-10.6-universal/egg/vcf creating build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/1kg.vcf.gz -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/init.py -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/bcftools.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/example-4.0.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/example-4.1-bnd.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/example-4.1-sv.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/example-4.1.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/freebayes.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/gatk.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/issue-16.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/issue_49.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/null_genotype_mono.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/prof.py -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/samtools.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/tb.vcf.gz -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/tb.vcf.gz.tbi -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/test_vcf.py -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/test/walk_left.vcf -> build/bdist.macosx-10.6-universal/egg/vcf/test copying build/lib.macosx-10.6-universal-2.6/vcf/utils.py -> build/bdist.macosx-10.6-universal/egg/vcf byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/init.py to init.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/filters.py to filters.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/model.py to model.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/parser.py to parser.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/test/init.py to init.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/test/prof.py to prof.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/test/test_vcf.py to test_vcf.pyc byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/utils.py to utils.pyc creating stub loader for vcf/cparse.so byte-compiling build/bdist.macosx-10.6-universal/egg/vcf/cparse.py to cparse.pyc creating build/bdist.macosx-10.6-universal/egg/EGG-INFO installing scripts to build/bdist.macosx-10.6-universal/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.macosx-10.6-universal/egg/EGG-INFO/scripts copying build/scripts-2.6/vcf_filter.py -> build/bdist.macosx-10.6-universal/egg/EGG-INFO/scripts copying build/scripts-2.6/vcf_melt -> build/bdist.macosx-10.6-universal/egg/EGG-INFO/scripts changing mode of build/bdist.macosx-10.6-universal/egg/EGG-INFO/scripts/vcf_filter.py to 755 changing mode of build/bdist.macosx-10.6-universal/egg/EGG-INFO/scripts/vcf_melt to 755 copying PyVCF.egg-info/PKG-INFO -> build/bdist.macosx-10.6-universal/egg/EGG-INFO copying PyVCF.egg-info/SOURCES.txt -> build/bdist.macosx-10.6-universal/egg/EGG-INFO copying PyVCF.egg-info/dependency_links.txt -> build/bdist.macosx-10.6-universal/egg/EGG-INFO copying PyVCF.egg-info/entry_points.txt -> build/bdist.macosx-10.6-universal/egg/EGG-INFO copying PyVCF.egg-info/requires.txt -> build/bdist.macosx-10.6-universal/egg/EGG-INFO copying PyVCF.egg-info/top_level.txt -> build/bdist.macosx-10.6-universal/egg/EGG-INFO writing build/bdist.macosx-10.6-universal/egg/EGG-INFO/native_libs.txt zip_safe flag not set; analyzing archive contents... vcf.test.test_vcf: module references file creating 'dist/PyVCF-0.5.0-py2.6-macosx-10.6-universal.egg' and adding 'build/bdist.macosx-10.6-universal/egg' to it removing 'build/bdist.macosx-10.6-universal/egg' (and everything under it) Processing PyVCF-0.5.0-py2.6-macosx-10.6-universal.egg removing '/Library/Python/2.6/site-packages/PyVCF-0.5.0-py2.6-macosx-10.6-universal.egg' (and everything under it) creating /Library/Python/2.6/site-packages/PyVCF-0.5.0-py2.6-macosx-10.6-universal.egg Extracting PyVCF-0.5.0-py2.6-macosx-10.6-universal.egg to /Library/Python/2.6/site-packages PyVCF 0.5.0 is already the active version in easy-install.pth Installing vcf_filter.py script to /usr/local/bin Installing vcf_melt script to /usr/local/bin
Installed /Library/Python/2.6/site-packages/PyVCF-0.5.0-py2.6-macosx-10.6-universal.egg Processing dependencies for PyVCF==0.5.0 Searching for distribute Reading http://pypi.python.org/simple/distribute/ Reading http://packages.python.org/distribute Best match: distribute 0.6.28 Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.28.tar.gz#md5=b400b532e33f78551e6847c1f5965e56 Processing distribute-0.6.28.tar.gz Running distribute-0.6.28/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ineIJE/distribute-0.6.28/egg-dist-tmp-wMDwTU Before install bootstrap. Scanning installed packages Setuptools installation detected at /Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg Egg installation Patching... Renaming /Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg into /Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg.OLD.1345709279.75 Patched done. Relaunching... Before install bootstrap. Scanning installed packages Setuptools installation detected at /Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg Egg installation Already patched. After install bootstrap. Don't have permissions to write /Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, skipping Creating /Library/Python/2.6/site-packages/setuptools-0.6c11-py2.6.egg-info Creating /Library/Python/2.6/site-packages/setuptools.pth Copying distribute-0.6.28-py2.6.egg to /Library/Python/2.6/site-packages Adding distribute 0.6.28 to easy-install.pth file Installing easy_install script to /usr/local/bin Installing easy_install-2.6 script to /usr/local/bin
Installed /Library/Python/2.6/site-packages/distribute-0.6.28-py2.6.egg Finished processing dependencies for PyVCF==0.5.0
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import PyVCF Traceback (most recent call last): File "
", line 1, in ImportError: No module named PyVCF
On Thu, Aug 23, 2012 at 9:05 AM, James Casbon [email protected]:
Can you try runing cython on vcf/cparse.pyx?
This should generate vcf/cparse.c and then the build will happen.
Perhaps I should just check in that file. I can't understand why it is not being built. Apologies!
Reply to this email directly or view it on GitHubhttps://github.com/jamescasbon/PyVCF/issues/69#issuecomment-7962679.
Got it - had to install ordereddict but after that I can import vcf with no issues. All sorted out.
Great thanks for this
and apologies for the newb issue.
On Thu, Aug 23, 2012 at 9:17 AM, Martijn Vermaat [email protected]:
The packages is "vcf" (egg is "PyVCF"), try:
import vcf
— Reply to this email directly or view it on GitHubhttps://github.com/jamescasbon/PyVCF/issues/69#issuecomment-7962874.
No, I think this is a real issue!
Need to work out why cython failed to be pulled in.
ok - if there's anything I can do to help, just let me know
On Thu, Aug 23, 2012 at 4:02 PM, James Casbon [email protected]:
No, I think this is a real issue!
Need to work out why cython failed to be pulled in.
— Reply to this email directly or view it on GitHubhttps://github.com/jamescasbon/PyVCF/issues/69#issuecomment-7972548.
For what it's worth, I see a similar issue when installing PyVCF via pip in a virtualenv (Centos 6.4, Python 2.7.4, pip 1.3.1). I can install from source without issues.
@osborne6 is that with or without cython installed? And by same error, you mean the missing cparse.c?
@jamescasbon - I just re-verified this morning. I created a virtualenv 'sandbox', installed cython, and then tried to install PyVCF, and it had the error about cparse.c missing.
I have no problems installing globally, only within virtualenv.
This seems to be a setuptools/cython job. It doesn't do the cythonizing of the pyx file.
In case someone tumble on this via google ;-) (Not sure if it is the correct place to put it, sorry) I had the same error and install cython before installing pyvcf and installation went ok.
Can't say if it is related but in OS X 10.9.1, Python 2.7.5 Cython 0.20.1, virtualenv 1.10.1 and pip 1.5.2, I get this error:
$ pip install --upgrade pyvcf
Downloading/unpacking pyvcf
Downloading PyVCF-0.6.6.tar.gz
Running setup.py (path:/Users/cborroto/.virtualenvs/sciencemodule-dev/build/pyvcf/setup.py) egg_info for package pyvcf
Requirement already up-to-date: distribute in ./.virtualenvs/sciencemodule-dev/lib/python2.7/site-packages (from pyvcf)
Requirement already up-to-date: setuptools>=0.7 in ./.virtualenvs/sciencemodule-dev/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 /Users/cborroto/.virtualenvs/sciencemodule-dev/bin/python -c "import setuptools, tokenize;__file__='/Users/cborroto/.virtualenvs/sciencemodule-dev/build/pyvcf/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/8j/mf70c1k911zb066hc76yg9bh0000gn/T/pip-Nzuuxa-record/install-record.txt --single-version-externally-managed --compile --install-headers /Users/cborroto/.virtualenvs/sciencemodule-dev/include/site/python2.7:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-intel-2.7
creating build/lib.macosx-10.9-intel-2.7/vcf
copying vcf/__init__.py -> build/lib.macosx-10.9-intel-2.7/vcf
copying vcf/filters.py -> build/lib.macosx-10.9-intel-2.7/vcf
copying vcf/model.py -> build/lib.macosx-10.9-intel-2.7/vcf
copying vcf/parser.py -> build/lib.macosx-10.9-intel-2.7/vcf
copying vcf/utils.py -> build/lib.macosx-10.9-intel-2.7/vcf
creating build/lib.macosx-10.9-intel-2.7/vcf/test
copying vcf/test/__init__.py -> build/lib.macosx-10.9-intel-2.7/vcf/test
copying vcf/test/prof.py -> build/lib.macosx-10.9-intel-2.7/vcf/test
copying vcf/test/test_vcf.py -> build/lib.macosx-10.9-intel-2.7/vcf/test
running egg_info
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 dependency_links to PyVCF.egg-info/dependency_links.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 /Users/cborroto/.virtualenvs/sciencemodule-dev/bin/python -c "import setuptools, tokenize;__file__='/Users/cborroto/.virtualenvs/sciencemodule-dev/build/pyvcf/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/8j/mf70c1k911zb066hc76yg9bh0000gn/T/pip-Nzuuxa-record/install-record.txt --single-version-externally-managed --compile --install-headers /Users/cborroto/.virtualenvs/sciencemodule-dev/include/site/python2.7 failed with error code 1 in /Users/cborroto/.virtualenvs/sciencemodule-dev/build/pyvcf
Storing debug log for failure in /Users/cborroto/.pip/pip.log
Still can't get this to be repeatable. Running cython manually seems to be the way to do it.
This shouldn't be closed... it's still happening
I just tried to install pyvcf with pip in a virtualenv that already had Cython installed, and got the same error (Python 2.6). If it can't install via pip, then deploying it will be a pain for a lot of people.
error: can't copy 'vcf/cparse.pyx': doesn't exist or not a regular file
I'm sorry that I'm not really all that familiar with how Cython works on installation.
If I do a fresh install of pyvcf in a blank virtualenv (w/o cython), it works properly.
If I install Cython first, I get the error.
EDIT - Yes. I tried with python2, and was able to install cleanly with pip install.
I'm using python3.3 (perhaps python2 is needed?), and I get the same error
$ pip install pyvcf Downloading/unpacking pyvcf Downloading PyVCF-0.6.6.tar.gz Running setup.py egg_info for package pyvcf
Downloading/unpacking distribute (from pyvcf) Downloading distribute-0.7.3.zip (145kB): 145kB downloaded Running setup.py egg_info for package distribute
Requirement already satisfied (use --upgrade to upgrade): setuptools>=0.7 in /home/jeremiah/.virtualenvs/p3/lib/python3.3/site-packages (from distribute->pyvcf) Installing collected packages: pyvcf, distribute 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/jeremiah/.virtualenvs/p3/bin/python3 -c "import setuptools;__file__='/home/jeremiah/.virtualenvs/p3/build/pyvcf/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-dpr7ry-record/install-record.txt --single-version-externally-managed --install-headers /home/jeremiah/.virtualenvs/p3/include/site/python3.3:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.3
creating build/lib.linux-x86_64-3.3/vcf
copying vcf/utils.py -> build/lib.linux-x86_64-3.3/vcf
copying vcf/parser.py -> build/lib.linux-x86_64-3.3/vcf
copying vcf/init.py -> build/lib.linux-x86_64-3.3/vcf
copying vcf/filters.py -> build/lib.linux-x86_64-3.3/vcf
copying vcf/model.py -> build/lib.linux-x86_64-3.3/vcf
creating build/lib.linux-x86_64-3.3/vcf/test
copying vcf/test/test_vcf.py -> build/lib.linux-x86_64-3.3/vcf/test
copying vcf/test/init.py -> build/lib.linux-x86_64-3.3/vcf/test
copying vcf/test/prof.py -> build/lib.linux-x86_64-3.3/vcf/test
running egg_info
writing PyVCF.egg-info/PKG-INFO
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing requirements to PyVCF.egg-info/requires.txt
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...
This was on a Mac (10.8) with Python 2.7, setuptools v2.1
On Feb 20, 2014, at 5:33 AM, James Casbon [email protected] wrote:
Are you on RHEL? which version of setuptools have you got?
— Reply to this email directly or view it on GitHub.
Works for me! On Feb 21, 2014, at 2:22 AM, James Casbon [email protected] wrote:
@mbreese @cjav @jeremiahsavage please try 0.6.7
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I'm having the same problem described above when I try to install PyVCF on my mac:
sudo pip install pyvcf ... error: can't copy 'vcf/cparse.c': doesn't exist or not a regular file
But after reading the above thread, I still don't know what the solution is. How do I run cython manually on vcf/cparse.pyx?
I'm running python 2.7.3 on my mac (OS 10.9.4)
Thanks!
