On Fri, 30 Dec 2022 20:05:32 +0530 Nilesh Patra <nil...@debian.org> wrote: > Source: pairtools > Version: 0.3.0-3.2 > Severity: serious > > Pairtools FTBFS with pysam related error. Looks like > something is off. > > dh_auto_clean > I: pybuild base:240: python3.11 setup.py clean > Traceback (most recent call last): > > > File "/<<PKGBUILDDIR>>/setup.py", line 130, in <module> > ext_modules=get_ext_modules(), > ^^^^^^^^^^^^^^^^^ > File "/<<PKGBUILDDIR>>/setup.py", line 81, in get_ext_modules > extra_link_args=pysam.get_libraries(), > ^^^^^^^^^^^^^^^^^^^^^ > File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in > get_libraries > return [os.path.join(dirname, x + so) for x in pysam_libs] > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in > <listcomp> > return [os.path.join(dirname, x + so) for x in pysam_libs] > ~~^~~~ > TypeError: can only concatenate str (not "NoneType") to str
This patch in pysam gets the build in pairtools going beyond this point, but
now the build chokes with:
| pairtools.cli (unittest.loader._FailedTest.pairtools.cli) ... ERROR
| pairtools.lib (unittest.loader._FailedTest.pairtools.lib) ... ERROR
|
| ======================================================================
| ERROR: pairtools.cli (unittest.loader._FailedTest.pairtools.cli)
| ----------------------------------------------------------------------
| ImportError: Failed to import test module: pairtools.cli
| Traceback (most recent call last):
| File "/usr/lib/python3.11/unittest/loader.py", line 440, in _find_test_path
| package = self._get_module_from_name(name)
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| File "/usr/lib/python3.11/unittest/loader.py", line 350, in
_get_module_from_name
| __import__(name)
| File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pairtools/cli/__init__.py", line
188, in <module>
| from . import (
| File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pairtools/cli/dedup.py",
line 12, in <module>
| from ..lib import fileio, pairsam_format, headerops
| File
"/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pairtools/lib/__init__.py", line
7, in <module>
| from . import parse
| File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pairtools/lib/parse.py",
line 38, in <module>
| from .parse_pysam import get_mismatches_c
| ImportError:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/pairtools/lib/parse_pysam.cpython-311-x86_64-linux-gnu.so:
undefined symbol: bam_dup1
Description: Add patch to return proper sysconf so for current python
Author: Nilesh Patra <nil...@debian.org>
Last-Update: 2022-12-30
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -96,5 +96,7 @@
if pysam.config.HTSLIB == "builtin":
pysam_libs.append('libchtslib')
- so = sysconfig.get_config_var('SO')
+ so = sysconfig.get_config_var('EXT_SUFFIX')
+ if not so:
+ so = sysconfig.get_config_var('SO')
return [os.path.join(dirname, x + so) for x in pysam_libs]
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