Comments (8)
We don't have control on this, can you please report it on the FreeBSD issue tracker?
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We don't have control on this [...]
Why? Your project doesn't install these files.
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In 0.8.11:
- distutils is not a dependency any more
- a recent setuptools is needed to build the package
Maybe that helps?
from bx-python.
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
from bx-python.
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.
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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
.
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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.
from bx-python.
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'
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Related Issues (20)
- Extend linting with ruff
- Tests do not run in PEP517 out-of-source build (gentoo) HOT 5
- error can't found bx.intervals module
- get on bx.align.maf.MAFIndexedAccess results in wrong alignment blocks HOT 4
- Importing ABC directly from collections was deprecated and will be removed in Python 3.10. Use collections.abc
- time.clock has been removed in Python 3.8
- ImportError: undefined symbol: PyUnicodeUCS2_FromStringAndSize HOT 1
- binned_bitsets_from_list errors when chromosome size is larger than set MAX (512M) HOT 1
- Got wrong positions on chomped query maf subset HOT 2
- How to dealing with maf files compressed with bzip2 or lzop ? HOT 4
- Failed to load seekbzip2 module when dealing with bz2 files HOT 1
- undefined symbol: PyUnicodeUCS2_FromStringAndSize HOT 3
- documentation? HOT 3
- Add support to release linux aarch64 wheels HOT 1
- multiple sequence alignment
- upgrading bx-python to newer versions of python HOT 1
- ERROR Missing dependencies: oldest-supported-numpy HOT 2
- Build errors on osx-arm64 (bioconda) HOT 2
- 0.12.0: Fails to build: error: incompatible integer to pointer conversion assigning to 'void **' from 'int' HOT 1
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