Installation error: undefined symbol: PyFPE_jbuf

On an up to date Centos 7 installation, I can’t do anything to make this error go away. I understand that it shouldn’t effect our ability to run the software, but the error remains.

[root@slurm-01 cutadapt-1.9.1]# find . -name "*.pyc" -exec rm -rf {} \;
[root@slurm-01 cutadapt-1.9.1]# 
[root@slurm-01 cutadapt-1.9.1]# /usr/bin/python2.7 setup.py build_ext -i
running build_ext
[root@slurm-01 cutadapt-1.9.1]# bin/cutadapt --help

ERROR: A required extension module could not be imported because it is
incompatible with your system. A quick fix is to recompile the extension
modules with the following command:

    /usr/bin/python setup.py build_ext -i

See the documentation for alternative ways of installing the program.

The original error message follows.

Traceback (most recent call last):
  File "bin/cutadapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/config/binaries/cutadapt/cutadapt-1.9.1/cutadapt/scripts/cutadapt.py", line 62, in <module>
    check_importability()
  File "/config/binaries/cutadapt/cutadapt-1.9.1/cutadapt/__init__.py", line 9, in check_importability
    import cutadapt._align
ImportError: /config/binaries/cutadapt/cutadapt-1.9.1/cutadapt/_align.so: undefined symbol: PyFPE_jbuf
[root@slurm-01 cutadapt-1.9.1]# python2.7 bin/cutadapt --help

ERROR: A required extension module could not be imported because it is
incompatible with your system. A quick fix is to recompile the extension
modules with the following command:

    /usr/bin/python2.7 setup.py build_ext -i

See the documentation for alternative ways of installing the program.

The original error message follows.

Traceback (most recent call last):
  File "bin/cutadapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/config/binaries/cutadapt/cutadapt-1.9.1/cutadapt/scripts/cutadapt.py", line 62, in <module>
    check_importability()
  File "/config/binaries/cutadapt/cutadapt-1.9.1/cutadapt/__init__.py", line 9, in check_importability
    import cutadapt._align
ImportError: /config/binaries/cutadapt/cutadapt-1.9.1/cutadapt/_align.so: undefined symbol: PyFPE_jbuf
[root@slurm-01 cutadapt-1.9.1]# 

[datakid]

Ah! I ended up setting up with python setup.py install --prefix= and python3 setup.py install --prefix=, then having two modulefiles.

The important part in the modulefiles, to avoid this error

from cutadapt.scripts import cutadapt
ImportError: No module named cutadapt.scripts

is to setenv PYTHONPATH=$path/lib64/python[x]/site-packages/ and where necessary set-alias python '/usr/bin/python3'

[marcelm]

You can try pip3 install instead to get a cutadapt with multi-core support. (Which is only available on Python 3.)