[Debian-med-packaging] Bug#1075407: pybigwig: ftbfs with GCC-14

[Matthias Klose]

Package: src:pybigwig
Version: 0.3.22+dfsg-1
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/pybigwig_0.3.22+dfsg-1_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-14/porting_to.html

[...]
pyBigWig.c: In function ‘pyBwAddHeader’:
pyBigWig.c:897:32: error: passing argument 1 of ‘bwCreateChromList’ from incompatible pointer type [-Wincompatible-pointer-types]
  897 |     bw->cl = bwCreateChromList(chroms, lengths, n);
      |                                ^~~~~~
      |                                |
      |                                char **
In file included from pyBigWig.h:3,
                 from pyBigWig.c:3:
/usr/include/bigWig.h:497:51: note: expected ‘const char * const*’ but argument is of type ‘char **’
  497 | chromList_t *bwCreateChromList(const char* const* chroms, const uint32_t *lengths, int64_t n);
      |                                ~~~~~~~~~~~~~~~~~~~^~~~~~
pyBigWig.c: In function ‘PyAddIntervals’:
pyBigWig.c:1251:29: error: passing argument 2 of ‘bwAddIntervals’ from incompatible pointer type [-Wincompatible-pointer-types]
 1251 |     rv = bwAddIntervals(bw, cchroms, ustarts, uends, fvalues, n);
      |                             ^~~~~~~
      |                             |
      |                             char **
/usr/include/bigWig.h:524:57: note: expected ‘const char * const*’ but argument is of type ‘char **’
  524 | int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *start, const uint32_t *end, const float *values, uint32_t n);
      |                                      ~~~~~~~~~~~~~~~~~~~^~~~~
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3.11 setup.py build 
I: pybuild base:311: /usr/bin/python3 setup.py build 
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybigwig/build/pyBigWigTest
copying pyBigWigTest/test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybigwig/build/pyBigWigTest
copying pyBigWigTest/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybigwig/build/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-312
x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c pyBigWig.c -o build/temp.linux-x86_64-cpython-312/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);
      |            ^~~~~~~~~~~~~~~~~~~~~
pyBigWig.c: In function ‘pyBwAddHeader’:
pyBigWig.c:897:32: error: passing argument 1 of ‘bwCreateChromList’ from incompatible pointer type [-Wincompatible-pointer-types]
  897 |     bw->cl = bwCreateChromList(chroms, lengths, n);
      |                                ^~~~~~
      |                                |
      |                                char **
In file included from pyBigWig.h:3,
                 from pyBigWig.c:3:
/usr/include/bigWig.h:497:51: note: expected ‘const char * const*’ but argument is of type ‘char **’
  497 | chromList_t *bwCreateChromList(const char* const* chroms, const uint32_t *lengths, int64_t n);
      |                                ~~~~~~~~~~~~~~~~~~~^~~~~~
pyBigWig.c: In function ‘PyAddIntervals’:
pyBigWig.c:1251:29: error: passing argument 2 of ‘bwAddIntervals’ from incompatible pointer type [-Wincompatible-pointer-types]
 1251 |     rv = bwAddIntervals(bw, cchroms, ustarts, uends, fvalues, n);
      |                             ^~~~~~~
      |                             |
      |                             char **
/usr/include/bigWig.h:524:57: note: expected ‘const char * const*’ but argument is of type ‘char **’
  524 | int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *start, const uint32_t *end, const float *values, uint32_t n);
      |                                      ~~~~~~~~~~~~~~~~~~~^~~~~
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build 
dh_auto_build: error: pybuild --build -i python{version} -p "3.11 3.12" returned exit code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2