Question: Software testing process failure: How can I match the already installed programs with the testing data?
0
gravatar for caro-ca
8 days ago by
caro-ca0
caro-ca0 wrote:

Hi! I am running a software that detects transposons in a model organism, [Tepid][1]. Unfortunately TEPID doesn't offer user support. For this reason, I decided to post the issue here wondering if someone is familiar with the error message.

(base) silviav@wildtype1:~/TEPID:python setup.py test
running test
running egg_info
writing requirements to TEPID.egg-info/requires.txt
writing TEPID.egg-info/PKG-INFO
writing top-level names to TEPID.egg-info/top_level.txt
writing dependency_links to TEPID.egg-info/dependency_links.txt
reading manifest file 'TEPID.egg-info/SOURCES.txt'
writing manifest file 'TEPID.egg-info/SOURCES.txt'
running build_ext
Failure: ImportError (/home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so: undefined symbol: PyFPE_jbuf) ... ERROR

======================================================================
ERROR: Failure: ImportError (/home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so: undefined symbol: PyFPE_jbuf)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/silviav/anaconda2/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/silviav/anaconda2/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/silviav/anaconda2/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/silviav/TEPID/tests/tepid_test.py", line 3, in <module>
    from tepid import tepid
  File "/home/silviav/TEPID/tepid/tepid.py", line 9, in <module>
    import pybedtools
  File "/home/silviav/.local/lib/python2.7/site-packages/pybedtools/__init__.py", line 10, in <module>
    from .cbedtools import (
ImportError: /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so: undefined symbol: PyFPE_jbuf

----------------------------------------------------------------------
Ran 1 test in 0.101s

FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>

I thought maybe pybedtools was not installed but it is:

(base) silviav@wildtype1:~/TEPID:whereis pybedtools
pybedtools: /home/silviav/anaconda2/bin/pybedtools

Additionally, I installed TEPID with anaconda2 being activated and I don't know what could have gone wrong. I really would appreciate any help. Thank you in advance!

anaconda2 pybedtools • 121 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by caro-ca0
1

Please edit post title to make it concise/informative. Pasting an error message in the title is not good practice.

If this file present: ls -l /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so?

ADD REPLYlink modified 8 days ago • written 8 days ago by genomax80k

I already edited the title, hope it is informative enough, even though it was hard for me to find the accurate one.

The file also exists:

(base) silviav@wildtype1:~/TEPID:ls -l /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so
-rwxr-xr-x 1 silviav binf 2410168 Mar 20 12:50 /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so

Thank you for your help!

ADD REPLYlink written 8 days ago by caro-ca0
2
gravatar for genomax
8 days ago by
genomax80k
United States
genomax80k wrote:

Did you install tepid using bioconda? That should install all proper dependencies.

ADD COMMENTlink written 8 days ago by genomax80k

Thank you so much! I thought TEPID didn't have bioconda to install.

ADD REPLYlink written 8 days ago by caro-ca0

Dear @genomax, I don't know how to validate/close this question. It cannot find the green mark on the left.

ADD REPLYlink written 5 days ago by caro-ca0

I moved my comment to an answer. You should now be able to see the check mark under the vote count.

ADD REPLYlink written 5 days ago by genomax80k

@genomax I installed tepid through bioconda and this is the error message:

(base) silviav@wildtype1:~:tepid-discover
Traceback (most recent call last):
  File "/home/silviav/anaconda2/bin/tepid-discover", line 7, in <module>
    from tepid import tepid
  File "/home/silviav/anaconda2/lib/python2.7/site-packages/tepid/tepid.py", line 9, in <module>
    import pybedtools
  File "/home/silviav/.local/lib/python2.7/site-packages/pybedtools/__init__.py", line 10, in <module>
    from .cbedtools import (
ImportError: /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so: undefined symbol: PyFPE_jbuf


(base) silviav@wildtype1:~:ls -l /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so 
-rwxr-xr-x 1 silviav binf 2410168 Mar 20 12:50 /home/silviav/.local/lib/python2.7/site-packages/pybedtools/cbedtools.so

Hope you could help me out. Thanks in advance.

ADD REPLYlink modified 4 days ago • written 4 days ago by caro-ca0
1

You may have installed TEPID via conda, but the one you installed via pip is what's actually getting used. Please do the following:

PYTHONNOUSERSITE=True tepid-discover

The "PYTHONNOUSERSITE" part will prevent python for looking at anything under /home/silviav/.local.

ADD REPLYlink written 4 days ago by Devon Ryan94k

THank you so much for your help!! It worked!!

ADD REPLYlink modified 4 days ago • written 4 days ago by caro-ca0
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