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undefined symbol: hasEntries #45

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clemenshug opened this issue Oct 2, 2017 · 3 comments
Closed

undefined symbol: hasEntries #45

clemenshug opened this issue Oct 2, 2017 · 3 comments

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@clemenshug
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Using version 0.3.5 I'm getting this error when importing pyBigWig (Python 2.7.9 on Ubuntu 15.04):

ImportError: /home/chug/kaic_venv/local/lib/python2.7/site-packages/pyBigWig.so: undefined symbol: hasEntries

I installed it using the binary wheel from PyPI. The symbol hasEntries doesn't seem to be properly exported:

> readelf -a /home/chug/kaic_venv/local/lib/python2.7/site-packages/pyBigWig.so | grep hasEntries
000000216038  000600000007 R_X86_64_JUMP_SLO 0000000000000000 hasEntries + 0
      6: 0000000000000000     0 NOTYPE  GLOBAL DEFAULT  UND hasEntries
    100: 0000000000000000     0 NOTYPE  GLOBAL DEFAULT  UND hasEntries

Interestingly, when I install from source using pip install --no-binary :all: pyBigWig it works fine.
@dpryan79
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Sorry about this and the delayed reply. I'm posting a new version now with this fixed. The problem was due to the hasEntries() function being in an ifdef that's only used if numpy is present upon compilation. That was an accident on my part.

@dpryan79 dpryan79 mentioned this issue Oct 19, 2017
Merged
dpryan79 added a commit that referenced this issue Oct 19, 2017
@dpryan79
Merge pull request #46 from dpryan79/fix_hasEntries
b350a73 
hasEntries() was only defined if numpy was installed! Bump to 0.3.6. Fix #45
@dpryan79
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Version 0.3.6 is now available via pip install and should have this fixed.

@clemenshug
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Works great, thank you very much!

rmsds added a commit to epfl-scitas/spack that referenced this issue Jan 24, 2019
@rmsds
pybigwig: add missing numpy dependency
a5cede3 
* (in particular up to 0.3.6) the build fails if numpy is not present
* deeptools/pyBigWig#45
rmsds added a commit to epfl-scitas/spack that referenced this issue Jan 25, 2019
@rmsds
pybigwig: add missing numpy dependency
962cc66 
* (in particular up to 0.3.6) the build fails if numpy is not present
* deeptools/pyBigWig#45
alalazo pushed a commit to epfl-scitas/spack that referenced this issue Jan 28, 2019
@rmsds @alalazo
Deeptools dependencies fixes (#227)
d711028 
* bcftools: use spack-built htslib

* instead of (re)building the bundled htslib it uses the already
installed one
* besides being sensible, it makes the build succeed with %intel

* pybigwig: add missing numpy dependency

* (in particular up to 0.3.6) the build fails if numpy is not present
* deeptools/pyBigWig#45

* py-pybigwig: update version

* py-pybigwig: fix building with python 3 and curl

* added a patch so that building with python3 and external curl works (it was previously picking up libcurl from the system)
* added the current version as limit for this patch as the fix is
also being pushed upstream
* deeptools/pyBigWig#76

* py-pybigwig: only apply patch when really needed

* in line with upstream PR
  * spack#10444
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@dpryan79 @clemenshug