Control: severity -1 normal Control: retitle -1 pairtools -- current repo in salsa FTBFS Control: clone -1 -2 Control: reassign -2 python3-pysam 0.20.0+ds-2 Control: retitle -2 pysam -- no definition for bam_dup1
On Fri, Dec 30, 2022 at 08:24:42PM +0530, Nilesh Patra wrote:
> 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
Turns out this is because there is just a function "declaration" in
pysam/libchtslib.pxd for bam_dup1.
But the headers imported do not even have the function.
I patched the current package in salsa to get the ball rolling. But this needs
bioframe.
Also, the below patch still needs to be applied to pysam. pushed to salsa.
> 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]
>
--
Best,
Nilesh
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