Your message dated Thu, 11 Dec 2025 21:58:16 +0000
with message-id <[email protected]>
and subject line Bug#1122457: fixed in pybigwig 0.3.23+dfsg-2
has caused the Debian Bug report #1122457,
regarding pybigwig: FTBFS: collect2: error: ld returned 1 exit status
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1122457: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1122457
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:pybigwig
Version: 0.3.23+dfsg-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202512/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:pybigwig, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:131: Building wheel for python3.14 with "build"
module
I: pybuild base:317: python3.14 -m build --skip-dependency-check --no-isolation
--wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybigwig
* Building wheel...
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82:
SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
!!
********************************************************************************
Please use a simple string containing a SPDX expression for
`project.license`. You can also use `project.license-files`. (Both options
available on setuptools>=77.0.0).
By 2026-Feb-18, you need to update your project and remove deprecated
calls
or your builds will no longer be supported.
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
corresp(dist, value, root_dir)
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX
license expression:
License :: OSI Approved
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
dist._finalize_license_expression()
/usr/lib/python3/dist-packages/setuptools/dist.py:759:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX
license expression:
License :: OSI Approved
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
self._finalize_license_expression()
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-314/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.linux-x86_64-cpython-314/pyBigWigTest
copying pyBigWigTest/__init__.py ->
build/lib.linux-x86_64-cpython-314/pyBigWigTest
running egg_info
creating pyBigWig.egg-info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '**/*.h'
adding license file 'LICENSE.txt'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
running build_ext
building 'pyBigWig' extension
creating build/temp.linux-x86_64-cpython-314
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITHNUMPY
-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig
-I/usr/include/python3.14
-I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.14 -c pyBigWig.c -o
build/temp.linux-x86_64-cpython-314/pyBigWig.o
pyBigWig.c: In function âPyString_AsStringâ:
pyBigWig.c:773:12: warning: return discards âconstâ qualifier from pointer
target type [-Wdiscarded-qualifiers]
773 | return PyUnicode_AsUTF8(obj);
| ^~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g
-fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-314/pyBigWig.o -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/python3.14/config-3.14-x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/../lib
-L/usr/lib/x86_64-linux-gnu -lBigWig -lm -lz -lpython3.14 -lcurl -lnpymath -o
build/lib.linux-x86_64-cpython-314/pyBigWig.cpython-314-x86_64-linux-gnu.so
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libBigWig.a(io.o): warning: relocation
against `stderr@@GLIBC_2.2.5' in read-only section `.text'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libBigWig.a(bwValues.o): relocation
R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making
a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
error: command '/usr/bin/x86_64-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:
python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybigwig
I: pybuild plugin_pyproject:131: Building wheel for python3.13 with "build"
module
I: pybuild base:317: python3.13 -m build --skip-dependency-check --no-isolation
--wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybigwig
* Building wheel...
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82:
SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
!!
********************************************************************************
Please use a simple string containing a SPDX expression for
`project.license`. You can also use `project.license-files`. (Both options
available on setuptools>=77.0.0).
By 2026-Feb-18, you need to update your project and remove deprecated
calls
or your builds will no longer be supported.
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
corresp(dist, value, root_dir)
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX
license expression:
License :: OSI Approved
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
dist._finalize_license_expression()
/usr/lib/python3/dist-packages/setuptools/dist.py:759:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX
license expression:
License :: OSI Approved
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
self._finalize_license_expression()
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-313/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.linux-x86_64-cpython-313/pyBigWigTest
copying pyBigWigTest/__init__.py ->
build/lib.linux-x86_64-cpython-313/pyBigWigTest
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '**/*.h'
adding license file 'LICENSE.txt'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
running build_ext
building 'pyBigWig' extension
creating build/temp.linux-x86_64-cpython-313
x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITHNUMPY
-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig
-I/usr/include/python3.13
-I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include
-I/usr/include/python3.13 -c pyBigWig.c -o
build/temp.linux-x86_64-cpython-313/pyBigWig.o
pyBigWig.c: In function âPyString_AsStringâ:
pyBigWig.c:773:12: warning: return discards âconstâ qualifier from pointer
target type [-Wdiscarded-qualifiers]
773 | return PyUnicode_AsUTF8(obj);
| ^~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g
-fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-313/pyBigWig.o -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/python3.13/config-3.13-x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/../lib
-L/usr/lib/x86_64-linux-gnu -lBigWig -lm -lz -lpython3.13 -lcurl -lnpymath -o
build/lib.linux-x86_64-cpython-313/pyBigWig.cpython-313-x86_64-linux-gnu.so
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libBigWig.a(io.o): warning: relocation
against `stderr@@GLIBC_2.2.5' in read-only section `.text'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libBigWig.a(bwValues.o): relocation
R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making
a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
error: command '/usr/bin/x86_64-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_pybigwig
dh_auto_build: error: pybuild --build -i python{version} -p "3.14 3.13"
returned exit code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: pybigwig
Source-Version: 0.3.23+dfsg-2
Done: Stuart Prescott <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pybigwig, 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.
Stuart Prescott <[email protected]> (supplier of updated pybigwig 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: Fri, 12 Dec 2025 08:18:31 +1100
Source: pybigwig
Architecture: source
Version: 0.3.23+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Stuart Prescott <[email protected]>
Closes: 1122457
Changes:
pybigwig (0.3.23+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Build against fixed libbigwig0t64 (Closes: #1122457).
* Update Standards-Version to 4.7.2 (no changes required).
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