0.8.11 Doesn't install some built shared libraries

[yurivict]

I am getting this error from the FreeBSD ports framework:

====> Checking for pkg-plist issues (check-plist)
===> Parsing plist
===> Checking for items in STAGEDIR missing from pkg-plist
===> Checking for items in pkg-plist which are not in STAGEDIR
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/_seqmapping.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/align/_core.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/align/_epo.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/align/sitemask/_cpg.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/arrays/array_tree.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/arrays/bed.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/arrays/wiggle.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/bbi/bbi_file.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/bbi/bigbed_file.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/bbi/bigwig_file.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/bbi/bpt_file.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/bbi/cirtree_file.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/bitset.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/intervals/cluster.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/intervals/intersection.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/intseq/ngramcount.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/misc/_seekbzip2.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/misc/bgzf.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/motif/_pwm.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/pwm/_position_weight_matrix.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/seq/_nib.so
Error: Missing: %%PYTHON_SITELIBDIR%%/7/bx-python-0.8.11/lib/bx/seq/_twobit.so
===> Error: Plist issues found.

The above listed shared libraries were built, written into plist, but were not installed.

Python 3.7
FreeBSD 12.2

[nsoranzo]

We don't have control on this, can you please report it on the FreeBSD issue tracker?

[yurivict]

We don't have control on this [...]

Why? Your project doesn't install these files.

[nsoranzo]

In 0.8.11:

• distutils is not a dependency any more
• a recent setuptools is needed to build the package

Maybe that helps?

[yurivict]

distutils is not a dependency any more

But python setup.py install is still recommended in the README file, and setup.py contains:
from distutils.core import Command

[nsoranzo]

Sorry, I confused myself there. You are right distutils is still used, although it's technically part of the Python standard library even if distributions tend to package it separately.
What is not needed any more is setuptools at runtime, it's only required (at version >=39.2.0) at install time.

python -m pip install . is the best way to install bx-python from source nowadays.

[yurivict]

python -m pip install wouldn't work for the bx-python port that I maintain. Ports should be built using setuptools.

There is a bug in the project that fails to install these files via setuptools.

[nsoranzo]

OK, I tracked this down, should be fixed by commit cd3cf73 .
Hopefully this works for you and you can cherry-pick it to your build system. Otherwise I can tag a new release.

[brobr]

Thanks, this was also needed for making a slackware package (also works via setup.py).
It solved the problem encountered with RSeQC:

Traceback (most recent call last):
File "/usr/bin/bam_stat.py", line 22, in
from bx.bitset import *
ModuleNotFoundError: No module named 'bx.bitset'