[Debian-med-packaging] Bug#1117756: libslow5lib: FTBFS: Segmentation fault
Santiago Vila
sanvila at debian.org
Fri Oct 10 17:27:24 BST 2025
Package: src:libslow5lib
Version: 0.7.0+dfsg-3
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/202510/
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:libslow5lib, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3 --buildsystem=cmake
dh_auto_clean -O--buildsystem=cmake
dh_autoreconf_clean -O--buildsystem=cmake
dh_clean -O--buildsystem=cmake
debian/rules binary
dh binary --with python3 --buildsystem=cmake
dh_update_autotools_config -O--buildsystem=cmake
dh_autoreconf -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-DSLOW5_USE_ZSTD="ON"
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DSLOW5_USE_ZSTD=ON ..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 15.2.0
-- The CXX compiler identification is GNU 15.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (0.3s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_FIND_USE_PACKAGE_REGISTRY
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
dh_auto_configure --buildsystem=pybuild
I: pybuild base:311: dh_auto_configure --buildsystem=cmake --builddirectory=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_slow5/build -- -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.13 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.13 -DPython_EXECUTABLE=/usr/bin/python3.13 -DPython_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython_INCLUDE_DIR=/usr/include/python3.13 -DPython3_EXECUTABLE=/usr/bin/python3.13 -DPython3_LIBRARY=/usr/lib/python3.13/config-3.13-x86_64-linux-gnu/libpython3.13.so -DPython3_INCLUDE_DIR=/usr/include/python3.13
cd .pybuild/cpython3_3.13_slow5/build && PKG_CONFIG=/usr/bi [too-long-redacted] usr/include/python3.13 ../../..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 15.2.0
-- The CXX compiler identification is GNU 15.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (0.3s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_FIND_USE_PACKAGE_REGISTRY
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
PYTHON_EXECUTABLE
PYTHON_INCLUDE_DIR
PYTHON_LIBRARY
Python3_EXECUTABLE
Python3_INCLUDE_DIR
Python3_LIBRARY
Python_EXECUTABLE
Python_INCLUDE_DIR
Python_LIBRARY
-- Build files have been written to: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_slow5/build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/slow5_static.dir/build.make CMakeFiles/slow5_static.dir/depend
make -f CMakeFiles/slow5.dir/build.make CMakeFiles/slow5.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/slow5_static.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/slow5.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f CMakeFiles/slow5.dir/build.make CMakeFiles/slow5.dir/build
make -f CMakeFiles/slow5_static.dir/build.make CMakeFiles/slow5_static.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 10%] Building C object CMakeFiles/slow5_static.dir/src/slow5.c.o
[ 20%] Building C object CMakeFiles/slow5.dir/src/slow5.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5.c.o -MF CMakeFiles/slow5_static.dir/src/slow5.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5.c.o -c /<<PKGBUILDDIR>>/src/slow5.c
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5.c.o -MF CMakeFiles/slow5.dir/src/slow5.c.o.d -o CMakeFiles/slow5.dir/src/slow5.c.o -c /<<PKGBUILDDIR>>/src/slow5.c
[ 30%] Building C object CMakeFiles/slow5_static.dir/src/slow5_idx.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_idx.c.o -MF CMakeFiles/slow5_static.dir/src/slow5_idx.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5_idx.c.o -c /<<PKGBUILDDIR>>/src/slow5_idx.c
[ 40%] Building C object CMakeFiles/slow5.dir/src/slow5_idx.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_idx.c.o -MF CMakeFiles/slow5.dir/src/slow5_idx.c.o.d -o CMakeFiles/slow5.dir/src/slow5_idx.c.o -c /<<PKGBUILDDIR>>/src/slow5_idx.c
[ 50%] Building C object CMakeFiles/slow5_static.dir/src/slow5_misc.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_misc.c.o -MF CMakeFiles/slow5_static.dir/src/slow5_misc.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5_misc.c.o -c /<<PKGBUILDDIR>>/src/slow5_misc.c
[ 60%] Building C object CMakeFiles/slow5.dir/src/slow5_misc.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_misc.c.o -MF CMakeFiles/slow5.dir/src/slow5_misc.c.o.d -o CMakeFiles/slow5.dir/src/slow5_misc.c.o -c /<<PKGBUILDDIR>>/src/slow5_misc.c
[ 70%] Building C object CMakeFiles/slow5_static.dir/src/slow5_press.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5_static.dir/src/slow5_press.c.o -MF CMakeFiles/slow5_static.dir/src/slow5_press.c.o.d -o CMakeFiles/slow5_static.dir/src/slow5_press.c.o -c /<<PKGBUILDDIR>>/src/slow5_press.c
[ 80%] Building C object CMakeFiles/slow5.dir/src/slow5_press.c.o
/usr/bin/cc -D_GLIBCXX_DEBUG -Dslow5_EXPORTS -I/<<PKGBUILDDIR>>/include -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 -g -Wall -O2 -std=c99 -fPIC -DSLOW5_USE_ZSTD -MD -MT CMakeFiles/slow5.dir/src/slow5_press.c.o -MF CMakeFiles/slow5.dir/src/slow5_press.c.o.d -o CMakeFiles/slow5.dir/src/slow5_press.c.o -c /<<PKGBUILDDIR>>/src/slow5_press.c
[ 90%] Linking C static library libslow5_static.a
/usr/bin/cmake -P CMakeFiles/slow5_static.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/slow5_static.dir/link.txt --verbose=1
/usr/bin/ar qc libslow5_static.a CMakeFiles/slow5_static.dir/src/slow5.c.o CMakeFiles/slow5_static.dir/src/slow5_idx.c.o CMakeFiles/slow5_static.dir/src/slow5_misc.c.o CMakeFiles/slow5_static.dir/src/slow5_press.c.o
/usr/bin/ranlib libslow5_static.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 90%] Built target slow5_static
[100%] Linking C shared library libslow5.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/slow5.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -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 -g -Wall -O2 -std=c99 -Wl,--dependency-file=CMakeFiles/slow5.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libslow5.so.0 -o libslow5.so.0 CMakeFiles/slow5.dir/src/slow5.c.o CMakeFiles/slow5.dir/src/slow5_idx.c.o CMakeFiles/slow5.dir/src/slow5_misc.c.o CMakeFiles/slow5.dir/src/slow5_press.c.o -lzstd
/usr/bin/cmake -E cmake_symlink_library libslow5.so.0 libslow5.so.0 libslow5.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[100%] Built target slow5
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
for py in `py3versions -s`; do \
$py setup.py build; \
done
/usr/lib/python3/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
/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 :: MIT License
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
self._finalize_license_expression()
running build
running build_ext
Compiling python/pyslow5.pyx because it changed.
[1/1] Cythonizing python/pyslow5.pyx
building 'pyslow5' extension
creating build/temp.linux-x86_64-cpython-313/python
creating build/temp.linux-x86_64-cpython-313/src
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 -Iinclude/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c python/pyslow5.c -o build/temp.linux-x86_64-cpython-313/python/pyslow5.o -g -Wall -O2 -std=c99
python/pyslow5.c: In function ‘__pyx_pf_7pyslow5_4Open_60write_record’:
python/pyslow5.c:42769:10: warning: ‘__pyx_v_ret’ may be used uninitialized [-Wmaybe-uninitialized]
42769 | if (__pyx_t_7) {
| ^
python/pyslow5.c:40525:8: note: ‘__pyx_v_ret’ was declared here
40525 | long __pyx_v_ret;
| ^~~~~~~~~~~
python/pyslow5.c: In function ‘__pyx_pf_7pyslow5_4Open_62write_record_batch’:
python/pyslow5.c:46876:14: warning: ‘__pyx_v_ret’ may be used uninitialized [-Wmaybe-uninitialized]
46876 | if (__pyx_t_5) {
| ^
python/pyslow5.c:43380:8: note: ‘__pyx_v_ret’ was declared here
43380 | long __pyx_v_ret;
| ^~~~~~~~~~~
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 -Iinclude/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c python/slow5threads.c -o build/temp.linux-x86_64-cpython-313/python/slow5threads.o -g -Wall -O2 -std=c99
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 -Iinclude/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c src/slow5.c -o build/temp.linux-x86_64-cpython-313/src/slow5.o -g -Wall -O2 -std=c99
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 -Iinclude/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c src/slow5_idx.c -o build/temp.linux-x86_64-cpython-313/src/slow5_idx.o -g -Wall -O2 -std=c99
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 -Iinclude/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c src/slow5_misc.c -o build/temp.linux-x86_64-cpython-313/src/slow5_misc.o -g -Wall -O2 -std=c99
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 -Iinclude/ -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c src/slow5_press.c -o build/temp.linux-x86_64-cpython-313/src/slow5_press.o -g -Wall -O2 -std=c99
creating build/lib.linux-x86_64-cpython-313
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/python/pyslow5.o build/temp.linux-x86_64-cpython-313/python/slow5threads.o build/temp.linux-x86_64-cpython-313/src/slow5.o build/temp.linux-x86_64-cpython-313/src/slow5_idx.o build/temp.linux-x86_64-cpython-313/src/slow5_misc.o build/temp.linux-x86_64-cpython-313/src/slow5_press.o -L. -L/usr/lib/x86_64-linux-gnu -lm -lz -lstreamvbyte -o build/lib.linux-x86_64-cpython-313/pyslow5.cpython-313-x86_64-linux-gnu.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p lib
cp -a obj-x86_64-linux-gnu/libslow5_static.a lib/libslow5.a
/usr/bin/make -C test zstd=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
mkdir bin
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ endian_test.c -o bin/endian_test -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_helpers.c -o bin/unit_test_helpers -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_press.c -o bin/unit_test_press -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_ascii.c -o bin/unit_test_ascii -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_binary.c -o bin/unit_test_binary -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ convert_slow5_test.c -o bin/convert_slow5_test -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_two_rg.c -o bin/unit_test_two_rg -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_lossless.c -o bin/unit_test_lossless -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_empty.c -o bin/unit_test_empty -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -Werror -std=gnu99 -DSLOW5_USE_ZSTD -Wdate-time -D_FORTIFY_SOURCE=2 -I ../include/ -I ../src/ unit_test_enum.c -o bin/unit_test_enum -Wl,-z,relro -Wl,-z,now ../lib/libslow5.a -lm -lz -lstreamvbyte -lzstd
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
for pys in `py3versions -s`; do \
echo $pys; \
pydir=`$pys debian/get-pyver-dir.py`; \
echo $pydir; X=0; \
PYTHONPATH=`pwd`/build/$pydir $pys -m unittest -v python/test.py || X=$?; \
if [ "" != 0 ]; then exit $X; fi; \
done
python3.13
lib.linux-x86_64-cpython-313
test_nonExistant_aux (python.test.TestAUX.test_nonExistant_aux) ... [slow5_idx_init::INFO][1;34m Index file not found. Creating an index at 'examples/example2.slow5.idx'.[0m
10-Oct-25 13:27:12 - [WARNING]: get_read unknown aux name: noExistTest
ERROR
test_read_id (python.test.TestAUX.test_read_id) ... 10-Oct-25 13:27:12 - [WARNING]: get_read unknown aux name: noExistTest
ERROR
test_read_number (python.test.TestAUX.test_read_number) ... 10-Oct-25 13:27:12 - [WARNING]: get_read unknown aux name: noExistTest
ERROR
test_start_mux (python.test.TestAUX.test_start_mux) ... 10-Oct-25 13:27:12 - [WARNING]: get_read unknown aux name: noExistTest
ERROR
test_get_aux_names (python.test.TestAuxAll.test_get_aux_names) ... ok
test_get_aux_types (python.test.TestAuxAll.test_get_aux_types) ... ok
test_get_read_all_aux (python.test.TestAuxAll.test_get_read_all_aux) ... ERROR
test_seq_reads_pA_aux_all (python.test.TestAuxAll.test_seq_reads_pA_aux_all) ... ERROR
test_class_methods (python.test.TestBase.test_class_methods) ... [slow5_idx_init::INFO][1;34m Index file not found. Creating an index at 'examples/example.slow5.idx'.[0m
ERROR
test_digitisation (python.test.TestBase.test_digitisation) ... ERROR
test_len_raw_signal (python.test.TestBase.test_len_raw_signal) ... ERROR
test_offset (python.test.TestBase.test_offset) ... ERROR
test_pylen_signal (python.test.TestBase.test_pylen_signal) ... ERROR
test_range (python.test.TestBase.test_range) ... ERROR
test_read_group (python.test.TestBase.test_read_group) ... ERROR
test_read_id (python.test.TestBase.test_read_id) ... ERROR
test_read_type (python.test.TestBase.test_read_type) ... ERROR
test_sampling_rate (python.test.TestBase.test_sampling_rate) ... ERROR
test_signal (python.test.TestBase.test_signal) ... ERROR
test_get_all_headers (python.test.TestHeaders.test_get_all_headers) ... ok
test_get_header_names (python.test.TestHeaders.test_get_header_names) ... ok
test_digitisation (python.test.TestRandomAccess.test_digitisation) ... ERROR
test_len_raw_signal (python.test.TestRandomAccess.test_len_raw_signal) ... ERROR
test_offset (python.test.TestRandomAccess.test_offset) ... ERROR
test_pylen_signal (python.test.TestRandomAccess.test_pylen_signal) ... ERROR
test_range (python.test.TestRandomAccess.test_range) ... ERROR
test_read_group (python.test.TestRandomAccess.test_read_group) ... ERROR
test_read_id (python.test.TestRandomAccess.test_read_id) ... ERROR
test_sampling_rate (python.test.TestRandomAccess.test_sampling_rate) ... ERROR
test_signal (python.test.TestRandomAccess.test_signal) ... ERROR
test_seq_reads (python.test.TestSequentialRead.test_seq_reads) ... ERROR
test_get_empty_header (python.test.TestWrite.test_get_empty_header) ... ok
test_get_empty_record (python.test.TestWrite.test_get_empty_record) ... ok
test_write_header (python.test.TestWrite.test_write_header) ... ok
test_write_records (python.test.TestWrite.test_write_records) ... ERROR
test_get_empty_aux (python.test.TestWriteAux.test_get_empty_aux) ... ok
test_write_records_aux (python.test.TestWriteAux.test_write_records_aux) ... ERROR
test_write_matches_read (python.test.TestWriteData.test_write_matches_read) ... [slow5_hdr_init::ERROR][1;31m Malformed slow5 header. No newline character in whole file.[0m At src/slow5.c:678
[slow5_init::ERROR][1;31m Parsing slow5 header of file 'examples/example_write.slow5' failed.[0m At src/slow5.c:153
Segmentation fault
make[1]: *** [debian/rules:32: override_dh_auto_test] Error 139
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
More information about the Debian-med-packaging
mailing list