[Debian-med-packaging] Bug#1122457: pybigwig: FTBFS: collect2: error: ld returned 1 exit status
Santiago Vila
sanvila at debian.org
Wed Dec 10 20:40:26 GMT 2025
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 ‘PyString_AsString’:
pyBigWig.c:773:12: warning: return discards ‘const’ 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 ‘PyString_AsString’:
pyBigWig.c:773:12: warning: return discards ‘const’ 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
--------------------------------------------------------------------------------
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