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Groups > linux.debian.bugs.dist > #1130799 > unrolled thread
| Started by | Nilesh Patra <nilesh@debian.org> |
|---|---|
| First post | 2022-12-30 15:40 +0100 |
| Last post | 2023-01-08 20:10 +0100 |
| Articles | 4 — 2 participants |
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Bug#1027335: pairtools -- FTBFS in unstable Nilesh Patra <nilesh@debian.org> - 2022-12-30 15:40 +0100
Bug#1027335: pairtools -- FTBFS in unstable Nilesh Patra <nilesh@debian.org> - 2022-12-30 16:00 +0100
Bug#1027386: [Debian-med-packaging] Bug#1027335: pairtools -- FTBFS in unstable Nilesh Patra <nilesh@debian.org> - 2022-12-31 20:00 +0100
Bug#1027386: [Debian-med-packaging] Bug#1027335: pairtools -- FTBFS in unstable Étienne Mollier <emollier@emlwks999.eu> - 2023-01-08 20:10 +0100
| From | Nilesh Patra <nilesh@debian.org> |
|---|---|
| Date | 2022-12-30 15:40 +0100 |
| Subject | Bug#1027335: pairtools -- FTBFS in unstable |
| Message-ID | <FIoIa-elx5-9@gated-at.bofh.it> |
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
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
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| From | Nilesh Patra <nilesh@debian.org> |
|---|---|
| Date | 2022-12-30 16:00 +0100 |
| Message-ID | <FIp1v-elDX-7@gated-at.bofh.it> |
| In reply to | #1130799 |
[Multipart message — attachments visible in raw view] — view raw
On Fri, 30 Dec 2022 20:05:32 +0530 Nilesh Patra <nilesh@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 <nilesh@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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| From | Nilesh Patra <nilesh@debian.org> |
|---|---|
| Date | 2022-12-31 20:00 +0100 |
| Subject | Bug#1027386: [Debian-med-packaging] Bug#1027335: pairtools -- FTBFS in unstable |
| Message-ID | <FIPfj-eEmB-9@gated-at.bofh.it> |
| In reply to | #1130799 |
[Multipart message — attachments visible in raw view] — view raw
Hi Etienne, On Fri, 30 Dec 2022 16:01:00 +0100 =?utf-8?Q?=C3=89tienne?= Mollier <emollier@emlwks999.eu> wrote: > Nilesh Patra, on 2022-12-30: > > 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 > > 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 <module> > 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 <listcomp> > 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: I believe I have fixed this particular problem in next pysam upload. However, the issue with bam_dup1 and a bunch of other functions in pysam still remains. I had to hack around by applying this patch in pairtools https://salsa.debian.org/med-team/pairtools/-/blob/master/debian/patches/fix-pysam-ftbfs.patch IMHO this really is un-called for, as pysam should resolve these things. In particular, pysam declared in pysam/libchtslib.pxd and there are also a bunch of htslib imports in htslib_util.h but probably those function defs have been removed in those htslib headers. In particular we are likely bitten by htslib vers moving async with what pysam is expecting. These should be fixed prior to release I guess :) > $ python3.10 reproducer.py Curious -- what script is this? :) -- Best, Nilesh
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| From | Étienne Mollier <emollier@emlwks999.eu> |
|---|---|
| Date | 2023-01-08 20:10 +0100 |
| Subject | Bug#1027386: [Debian-med-packaging] Bug#1027335: pairtools -- FTBFS in unstable |
| Message-ID | <FLJdn-gwcO-1@gated-at.bofh.it> |
| In reply to | #1130979 |
[Multipart message — attachments visible in raw view] — view raw
Hi Nilesh, [I noticed this answer in my drafts quite late, sorry for the delay answering.] Nilesh Patra, on 2023-01-01: > On Fri, 30 Dec 2022 16:01:00 +0100 =?utf-8?Q?=C3=89tienne?= Mollier <emollier@emlwks999.eu> wrote: > > $ python3.10 reproducer.py > > Curious -- what script is this? :) This one, sorry my wording made it confusing: $ cat reproducer.py import pysam for lib in pysam.get_libraries(): print(lib) Have a nice day, :) -- Étienne Mollier <emollier@emlwks999.eu> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/4, please excuse my verbosity.
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