Undefined sysmbol in logprob.so

[cflsjt]

Hi @EhsanMotazedi - I'm finally getting a chance to play with your latest tool! I ran in to an issue though, maybe no biggie. I've git cloned recursively but upon running:

python main.py -h

I get this output

  File "main.py", line 17, in <module>
    from branchprune import BlockException, makePermutation, SetGenos, GetProbReads
  File "/powerplant/workspace/cflsjt/PopPoly/branchprune.py", line 13, in <module>
    from haplotypes import Haplotypes, getMEC
  File "/powerplant/workspace/cflsjt/PopPoly/haplotypes.py", line 12, in <module>
    from logprob import _xor, diffVec, Hamming
ImportError: /powerplant/workspace/cflsjt/PopPoly/logprob.so: undefined symbol: PyFPE_jbuf ```

[EhsanMotazedi]

HI Susan,

This error has indeed been reported by other users (including myself!). It has to do with numpy installation and I get it on one server while not not another. I have uploaded a new version of PopPoly in which I mention this error and give a link where it is discussed on StackOverflow. In the new version, one can explicitly specify the name of the parents. There is also a perl wrapper with extra options to use a bam file that contains multiple contigs by choosing the name of the desired contig for haplotyping, as well as to filtering SNPs upon genotype missing rate. Please have a look:

https://git.wageningenur.nl/motaz001/PopPoly

Cheers, Ehsan

Op wo 18 jul. 2018 om 06:52 schreef Susan Thomson <notifications@github.com

:

Hi @EhsanMotazedi https://github.com/EhsanMotazedi - I'm finally getting a chance to play with your latest tool! I ran in to an issue though, maybe no biggie. I've git cloned recursively but upon running:

python main.py -h

I get this output

File "main.py", line 17, in from branchprune import BlockException, makePermutation, SetGenos, GetProbReads File "/powerplant/workspace/cflsjt/PopPoly/branchprune.py", line 13, in from haplotypes import Haplotypes, getMEC File "/powerplant/workspace/cflsjt/PopPoly/haplotypes.py", line 12, in from logprob import _xor, diffVec, Hamming ImportError: /powerplant/workspace/cflsjt/PopPoly/logprob.so: undefined symbol: PyFPE_jbuf ```

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[cflsjt]

Hi Ehsan, thanks yes it looks like numpy. I'm still having some issues but we will try and set up a clean conda env to have a go with shortly. Let you know how it goes!

[timothymillar]

Hi @EhsanMotazedi I think this issue explains it.

It looks like the version(s) of CPython available through anaconda are compiled without the --with-fpectl.

The pre-compiled logprob.so and logprob2.so must have been compiled againt a version of CPython that does support fpectl (e.g the versions packaged in Ubuntu/Debian).

I remove logprob.so and logprob2.so and rebuilt them against Anacondas python and now the I can get the help text without issue.

[EhsanMotazedi]

@timothymillar Hi Timo, You are right just have to recompile using cythonize -i logprob.pyx and cythonize -i logprob2.pyx. Hope it works!