[Debian-med-packaging] Bug#1075607: unifrac: ftbfs with GCC-14

[Matthias Klose]

Package: src:unifrac
Version: 1.3-3
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/unifrac_1.3-3_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

[...]
running build_ext
Compiling SSU
building 'unifrac._api' extension
creating build
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/unifrac
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c unifrac/_api.c -o build/temp.linux-x86_64-cpython-311/unifrac/_api.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from unifrac/_api.c:1255:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
unifrac/_api.c: In function ‘__pyx_f_7unifrac_4_api_result_to_skbio_distance_matrix’:
unifrac/_api.c:23770:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
23770 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_14; __pyx_t_7+=1) {
      |                                 ^
unifrac/_api.c: In function ‘__pyx_f_7unifrac_4_api_construct_support_bptree’:
unifrac/_api.c:27151:32: error: assignment to ‘_Bool *’ from incompatible pointer type ‘__pyx_t_7unifrac_4_api_bool *’ {aka ‘unsigned char *’} [-Wincompatible-pointer-types]
27151 |   __pyx_v_sp_bptree->structure = __pyx_v_structure;
      |                                ^
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_unifrac/build/unifrac
copying unifrac/_methods.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
copying unifrac/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
copying unifrac/_meta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
copying unifrac/tests/test_api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
copying unifrac/tests/test_methods.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
copying unifrac/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/e1.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/t1.newick -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/crawford.group.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/e2.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/crawford.tre -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/test.faith.exp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/crawford.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/t2.newick -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
running build_ext
Compiling SSU
building 'unifrac._api' extension
creating build/temp.linux-x86_64-cpython-312
creating build/temp.linux-x86_64-cpython-312/unifrac
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 -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c unifrac/_api.c -o build/temp.linux-x86_64-cpython-312/unifrac/_api.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from unifrac/_api.c:1255:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
unifrac/_api.c: In function ‘__pyx_f_7unifrac_4_api_result_to_skbio_distance_matrix’:
unifrac/_api.c:23770:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
23770 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_14; __pyx_t_7+=1) {
      |                                 ^
unifrac/_api.c: In function ‘__pyx_f_7unifrac_4_api_construct_support_bptree’:
unifrac/_api.c:27151:32: error: assignment to ‘_Bool *’ from incompatible pointer type ‘__pyx_t_7unifrac_4_api_bool *’ {aka ‘unsigned char *’} [-Wincompatible-pointer-types]
27151 |   __pyx_v_sp_bptree->structure = __pyx_v_structure;
      |                                ^
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:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2