Error in MacOSX

[GoogleCodeExporter]

Hello, I'm trying running RSeQC on a Mac OSX 10.9

I have gcc, python 2.7, numpy and R.

I installed RSeQC 2.3.9 by typing:

sudo python setup.py install

Although it generates some warnings during compiling, it seems to be 
successfully installed (log attached).

However, when I ran

python -c "from qcmodule import SAM"

it gives the following error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/xichen/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-macosx-10.5-x86_64.egg/qcmodule/SAM.py", line 23, in <module>
    import pysam
  File "/Users/xichen/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-macosx-10.5-x86_64.egg/pysam/__init__.py", line 1, in <module>
    from csamtools import *
ImportError: 
dlopen(/Users/xichen/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-maco
sx-10.5-x86_64.egg/csamtools.so, 2): Symbol not found: ___ks_insertsort_heap
  Referenced from: /Users/xichen/anaconda/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-macosx-10.5-x86_64.egg/csamtools.so
  Expected in: dynamic lookup

Could you please have a look the potential problems?

Thank you.

Regards,
Xi

Original issue reported on code.google.com by dbr...@gmail.com on 26 Mar 2014 at 3:18

Attachments:

• log.txt

[GoogleCodeExporter]

Hi,

I have the same problem here.... Any solution?

best
Roland

Original comment by rarn...@kimlab.org on 28 May 2014 at 5:31

[GoogleCodeExporter]

Hi it turns out to be pysam's problem. Update pysam seems to fix the problem:

https://groups.google.com/forum/#!topic/rseqc-discuss/Liu9CwbUSi0

Thanks,

Xi

Original comment by dbr...@gmail.com on 29 May 2014 at 6:16