Not able to install htseq on Mac OS Yosemite

[biomrpaul]

After installing HTSeq on Mac OS X Yosemite v10.10.3 and running htseq-count, I get the error:

Traceback (most recent call last):
  File "/usr/local/bin/htseq-count", line 5, in <module>
    pkg_resources.run_script('HTSeq==0.6.1p1', 'htseq-count')
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 492, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 1350, in run_script
    execfile(script_filename, namespace, namespace)
  File "/Library/Python/2.7/site-packages/HTSeq-0.6.1p1-py2.7-macosx-10.10-intel.egg/EGG-INFO/scripts/htseq-count", line 3, in <module>
    import HTSeq.scripts.count
  File "/Library/Python/2.7/site-packages/HTSeq-0.6.1p1-py2.7-macosx-10.10-intel.egg/HTSeq/__init__.py", line 9, in <module>
    from _HTSeq import *
  File "_HTSeq.pyx", line 14, in init HTSeq._HTSeq (src/_HTSeq.c:34537)
  File "/Library/Python/2.7/site-packages/HTSeq-0.6.1p1-py2.7-macosx-10.10-intel.egg/HTSeq/StepVector.py", line 26, in <module>
    _StepVector = swig_import_helper()
  File "/Library/Python/2.7/site-packages/HTSeq-0.6.1p1-py2.7-macosx-10.10-intel.egg/HTSeq/StepVector.py", line 22, in swig_import_helper
    _mod = imp.load_module('_StepVector', fp, pathname, description)
ImportError: dlopen(/Library/Python/2.7/site-packages/HTSeq-0.6.1p1-py2.7-macosx-10.10-intel.egg/HTSeq/_StepVector.so, 2): no suitable image found.  Did find:
	/Library/Python/2.7/site-packages/HTSeq-0.6.1p1-py2.7-macosx-10.10-intel.egg/HTSeq/_StepVector.so: mach-o, but wrong architecture

I have installed HTSeq using the instructions on their site and using easy_install. Both resulted in the same error. Looking back at the build output, I noticed a warning that may help in figuring out whats going on.

ld: warning: ignoring file /opt/local/lib/gcc49/libstdc++.dylib, file was built for x86_64 which is not the architecture being linked (i386): /opt/local/lib/gcc49/libstdc++.dylib
ld: warning: ignoring file /opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2/libgcc.a, file was built for archive which is not the architecture being linked (i386): /opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2/libgcc.a
ld: warning: ignoring file /opt/local/lib/gcc49/libgcc_ext.10.5.dylib, missing required architecture i386 in file /opt/local/lib/gcc49/libgcc_ext.10.5.dylib (1 slices)

Any suggestions?

Thank you.

[Pirol]

Hi,

unfortunately, I got the same error message on OS X Yosemite and on OS X El Capitan
Did you find a solution for that problem?

Many thanks in advance!

[GenoMax]

Have you installed Xcode and the associated command line tools for Xcode?