Bug#1027335: pairtools -- FTBFS in unstable
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 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 "/<>/setup.py", line 130, in
> > ext_modules=get_ext_modules(),
> > ^
> > File "/<>/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
> >
> > 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
> "/<>/.pybuild/cpython3_3.11/build/pairtools/cli/__init__.py",
> line 188, in
> |from . import (
> | File
> "/<>/.pybuild/cpython3_3.11/build/pairtools/cli/dedup.py", line
> 12, in
> |from ..lib import fileio, pairsam_format, headerops
> | File
> "/<>/.pybuild/cpython3_3.11/build/pairtools/lib/__init__.py",
> line 7, in
> |from . import parse
> | File
> "/<>/.pybuild/cpython3_3.11/build/pairtools/lib/parse.py", line
> 38, in
> |from .parse_pysam import get_mismatches_c
> | ImportError:
> /<>/.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
> 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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Processed: Re: [Debian-med-packaging] Bug#1027335: pairtools -- FTBFS in unstable
Processing control commands: > tags -1 + confirmed Bug #1027335 [src:pairtools] pairtools -- FTBFS in unstable Added tag(s) confirmed. > reassign -1 src:python-pysam 0.20.0+ds-2 Bug #1027335 [src:pairtools] pairtools -- FTBFS in unstable Bug reassigned from package 'src:pairtools' to 'src:python-pysam'. No longer marked as found in versions pairtools/0.3.0-3.2. Ignoring request to alter fixed versions of bug #1027335 to the same values previously set Bug #1027335 [src:python-pysam] pairtools -- FTBFS in unstable Marked as found in versions python-pysam/0.20.0+ds-2. > affects -1 src:pairtools Bug #1027335 [src:python-pysam] pairtools -- FTBFS in unstable Added indication that 1027335 affects src:pairtools -- 1027335: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1027335 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#1027335: [Debian-med-packaging] Bug#1027335: pairtools -- FTBFS in unstable
Control: tags -1 + confirmed Control: reassign -1 src:python-pysam 0.20.0+ds-2 Control: affects -1 src:pairtools Hi Nilesh, Nilesh Patra, on 2022-12-30: > File "/<>/setup.py", line 130, in > ext_modules=get_ext_modules(), > ^ > File "/<>/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 > > return [os.path.join(dirname, x + so) for x in pysam_libs] > ~~^~~~ > TypeError: can only concatenate str (not "NoneType") to str Thanks for catching this, I confirm I can reproduce the error without pairtools in the loop. Given the reproducer.py below: import pysam for lib in pysam.get_libraries(): print(lib) I do get the error with python3.11: $ python3.11 reproducer.py Traceback (most recent call last): File "/home/emollier/tmp/reproducer.py", line 2, in for lib in 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 return [os.path.join(dirname, x + so) for x in pysam_libs] ~~^~~~ TypeError: can only concatenate str (not "NoneType") to str Besides, the error looks genuine since in python3.10, the output seems to return the expected result: $ python3.10 reproducer.py /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-310-x86_64-linux-gnu.so So I'm reassigning the issue accordingly. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/1, please excuse my verbosity. signature.asc Description: PGP signature
Bug#1027335: pairtools -- FTBFS in unstable
On Fri, 30 Dec 2022 20:05:32 +0530 Nilesh Patra 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 "/<>/setup.py", line 130, in
> ext_modules=get_ext_modules(),
> ^
> File "/<>/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
>
> 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
"/<>/.pybuild/cpython3_3.11/build/pairtools/cli/__init__.py", line
188, in
|from . import (
| File "/<>/.pybuild/cpython3_3.11/build/pairtools/cli/dedup.py",
line 12, in
|from ..lib import fileio, pairsam_format, headerops
| File
"/<>/.pybuild/cpython3_3.11/build/pairtools/lib/__init__.py", line
7, in
|from . import parse
| File "/<>/.pybuild/cpython3_3.11/build/pairtools/lib/parse.py",
line 38, in
|from .parse_pysam import get_mismatches_c
| ImportError:
/<>/.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
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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Bug#1027335: pairtools -- FTBFS in unstable
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 "/<>/setup.py", line 130, in ext_modules=get_ext_modules(), ^ File "/<>/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 return [os.path.join(dirname, x + so) for x in pysam_libs] ~~^~~~ TypeError: can only concatenate str (not "NoneType") to str Thanks, Nilesh -- System Information: Debian Release: bookworm/sid APT prefers testing APT policy: (990, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 6.0.0-6-amd64 (SMP w/8 CPU threads; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
