Your message dated Mon, 18 Nov 2024 23:01:38 +0000
with message-id <[email protected]>
and subject line Bug#1081672: fixed in pairtools 1.1.0-1
has caused the Debian Bug report #1081672,
regarding FTBFS with Python 3.13
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1081672: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1081672
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pairtools
Version: 1.0.3-1
Severity: normal
Tags: upstream
User: [email protected]
Usertags: python3.13
Forwarded: https://github.com/open2c/pairtools/issues/250
This package failed build from source when test-built against a version of
python3-defaults that includes 3.13 as a supported version.
To reproduce this issue, build against python3-defaults (python3-all-dev etc.)
from Debian experimental.
What's new in Python 3.13:
https://docs.python.org/3.13/whatsnew/3.13.html
Log snippet:
building 'pairtools.lib.parse_pysam' extension
aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall
-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security
-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-Ipairtools/lib -I/usr/lib/python3/dist-packages/pysam
-I/usr/lib/python3/dist-packages/pysam/include/samtools
-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include
-I/usr/lib/python3/dist-packages/numpy/core/include -c
/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.c -o
build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.o
aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g
-fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security
-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-aarch64-cpython-312/<<PKGBUILDDIR>>/pairtools/lib/parse_pysam.o
-L/usr/lib/aarch64-linux-gnu -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/parse_pysam.cpython-312-aarch64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-312-aarch64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-312-aarch64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-312-aarch64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcvcf.cpython-312-aarch64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-312-aarch64-linux-gnu.so
/usr/lib/python3/dist-packages/pysam/libctabix.cpython-312-aarch64-linux-gnu.so
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- --system=custom --test-args="export CURPY={interpreter}; \
cd {build_dir} && {interpreter} -m pytest -v"
I: pybuild base:311: export CURPY=python3.13; cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build && python3.13 -m pytest -v
============================= test session starts ==============================
platform linux -- Python 3.13.0rc2, pytest-8.3.2, pluggy-1.5.0 --
/usr/bin/python3.13
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build
configfile: pytest.ini
testpaths: tests
plugins: typeguard-4.3.0
collecting ... collected 17 items / 2 errors
==================================== ERRORS ====================================
___________________ ERROR collecting tests/test_headerops.py ___________________
ImportError while importing test module
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/tests/test_headerops.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_headerops.py:2: in <module>
from pairtools.lib import headerops
pairtools/lib/__init__.py:1: in <module>
from . import fileio
pairtools/lib/fileio.py:2: in <module>
import pipes
E ModuleNotFoundError: No module named 'pipes'
____________________ ERROR collecting tests/test_select.py _____________________
ImportError while importing test module
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/tests/test_select.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
tests/test_select.py:6: in <module>
from pairtools.lib import pairsam_format
pairtools/lib/__init__.py:1: in <module>
from . import fileio
pairtools/lib/fileio.py:2: in <module>
import pipes
E ModuleNotFoundError: No module named 'pipes'
=========================== short test summary info ============================
ERROR tests/test_headerops.py
ERROR tests/test_select.py
!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 2 errors in 0.50s ===============================
E: pybuild pybuild:389: test: plugin custom failed with: exit code=2: export
CURPY=python3.13; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build &&
python3.13 -m pytest -v
I: pybuild base:311: export CURPY=python3.12; cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build && python3.12 -m pytest -v
============================= test session starts ==============================
platform linux -- Python 3.12.6, pytest-8.3.2, pluggy-1.5.0 --
/usr/bin/python3.12
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
configfile: pytest.ini
testpaths: tests
plugins: typeguard-4.3.0
collecting ... collected 31 items
tests/test_dedup.py::test_mock_pairsam PASSED [ 3%]
tests/test_filterbycov.py::test_mock_pairs PASSED [ 6%]
tests/test_flip.py::test_flip PASSED [ 9%]
tests/test_header.py::test_generate PASSED [ 12%]
tests/test_headerops.py::test_make_standard_header PASSED [ 16%]
tests/test_headerops.py::test_samheaderops PASSED [ 19%]
tests/test_headerops.py::test_merge_pairheaders PASSED [ 22%]
tests/test_headerops.py::test_merge_different_pairheaders PASSED [ 25%]
tests/test_headerops.py::test_force_merge_pairheaders PASSED [ 29%]
tests/test_headerops.py::test_merge_samheaders PASSED [ 32%]
tests/test_headerops.py::test_merge_headers PASSED [ 35%]
tests/test_markasdup.py::test_mock_pairsam PASSED [ 38%]
tests/test_merge.py::test_mock_pairsam PASSED [ 41%]
tests/test_parse.py::test_python_version PASSED [ 45%]
tests/test_parse.py::test_mock_pysam PASSED [ 48%]
tests/test_parse.py::test_mock_pysam_parse_all PASSED [ 51%]
tests/test_parse2.py::test_mock_pysam_parse2_read PASSED [ 54%]
tests/test_parse2.py::test_mock_pysam_parse2_pair PASSED [ 58%]
tests/test_restrict.py::test_restrict PASSED [ 61%]
tests/test_scaling.py::test_scaling PASSED [ 64%]
tests/test_select.py::test_preserve PASSED [ 67%]
tests/test_select.py::test_equal PASSED [ 70%]
tests/test_select.py::test_csv PASSED [ 74%]
tests/test_select.py::test_wildcard PASSED [ 77%]
tests/test_select.py::test_regex PASSED [ 80%]
tests/test_select.py::test_chrom_subset PASSED [ 83%]
tests/test_select.py::test_remove_columns PASSED [ 87%]
tests/test_sort.py::test_mock_pairsam PASSED [ 90%]
tests/test_split.py::test_split PASSED [ 93%]
tests/test_stats.py::test_mock_pairsam PASSED [ 96%]
tests/test_stats.py::test_merge_stats PASSED [100%]
=============================== warnings summary ===============================
pairtools/lib/fileio.py:2
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/fileio.py:2:
DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13
import pipes
pairtools/lib/stats.py:928
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/pairtools/lib/stats.py:928:
SyntaxWarning: invalid escape sequence '\w'
"""Extract the name of the tile for each read name in the series
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================= 31 passed, 2 warnings in 38.56s ========================
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13
3.12" --system=custom "--test-args=export CURPY={interpreter}; cd {build_dir}
&& {interpreter} -m pytest -v" returned exit code 13
make[1]: *** [debian/rules:16: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit
status 2
--------------------------------------------------------------------------------
Build finished at 2024-09-13T17:00:09Z
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/712345/
This bug has been filed at "normal" severity, as we haven't started the
transition to add 3.13 as a supported version, yet. This will be raised to RC
as soon as that happens, hopefully well before trixie.
Thanks,
Stefano
--- End Message ---
--- Begin Message ---
Source: pairtools
Source-Version: 1.1.0-1
Done: Alexandre Detiste <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pairtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alexandre Detiste <[email protected]> (supplier of updated pairtools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 18 Nov 2024 22:23:36 +0100
Source: pairtools
Architecture: source
Version: 1.1.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Alexandre Detiste <[email protected]>
Closes: 1081672 1085765
Changes:
pairtools (1.1.0-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 1.1.0
* Vendor "the" pipes module that was removed from Python3.13
(Closes: #1081672)
* Patch-out SyntaxWarnings (Closes: #1085765 )
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