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 --------------------------------------------------------------------------------
