Your message dated Sun, 22 Sep 2024 12:49:16 +0000
with message-id <[email protected]>
and subject line Bug#1081624: fixed in python-bx 0.13.0-1
has caused the Debian Bug report #1081624,
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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--
1081624: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1081624
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-bx
Version: 0.12.0-1
Severity: normal
User: [email protected]
Usertags: python3.13
Forward: https://github.com/bxlab/bx-python/issues/102
This package failed build from source when test-built against a version of
python3-defaults that incudes 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:
[1/1] Cythonizing lib/bx/_seqmapping.pyx
building 'bx._seqmapping' 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
-I/usr/include/python3.13 -c lib/bx/_seqmapping.c -o
build/temp.linux-aarch64-cpython-313/lib/bx/_seqmapping.o
lib/bx/_seqmapping.c: In function
‘__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate’:
lib/bx/_seqmapping.c:3609:15: error: implicit declaration of function
‘PyObject_AsWriteBuffer’; did you mean ‘PyObject_GetBuffer’?
[-Wimplicit-function-declaration]
3609 | __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void
**)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1)))
__PYX_ERR(0, 54, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~~
| PyObject_GetBuffer
lib/bx/_seqmapping.c: In function
‘__pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate’:
lib/bx/_seqmapping.c:5309:15: error: implicit declaration of function
‘PyObject_AsReadBuffer’; did you mean ‘PyObject_GetBuffer’?
[-Wimplicit-function-declaration]
5309 | __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const
**)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1)))
__PYX_ERR(0, 134, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~
| PyObject_GetBuffer
error: command '/usr/bin/aarch64-linux-gnu-gcc' failed with exit code 1
ERROR Backend subprocess exited when trying to invoke build_wheel
E: pybuild pybuild:389: build: plugin pyproject failed with: exit code=1:
python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_bx-python
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/709365/
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: python-bx
Source-Version: 0.13.0-1
Done: Alexandre Detiste <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-bx, 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 python-bx 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: Sun, 22 Sep 2024 14:14:04 +0200
Source: python-bx
Architecture: source
Version: 0.13.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Alexandre Detiste <[email protected]>
Closes: 1081624
Changes:
python-bx (0.13.0-1) unstable; urgency=medium
.
* Team Upload
* New upstream version 0.13.0 (Closes: #1081624)
* Refresh patches
* Add build-depends on python3-pyparsing
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