[Debian-med-packaging] Bug#1075545: sumaclust: ftbfs with GCC-14

[Matthias Klose]

Package: src:sumaclust
Version: 1.0.36+ds-2
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/sumaclust_1.0.36+ds-2_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

[...]
make[1]: *** Waiting for unfinished jobs....
sumaclust.c: In function ‘printInBIOMformat’:
sumaclust.c:294:27: error: assignment to ‘struct <anonymous> **’ from incompatible pointer type ‘struct fastaSeqPtr *’ [-Wincompatible-pointer-types]
  294 |                         c = (*seq)->center;
      |                           ^
sumaclust.c: In function ‘printInOTUtableFormat’:
sumaclust.c:461:27: error: assignment to ‘struct <anonymous> **’ from incompatible pointer type ‘struct fastaSeqPtr *’ [-Wincompatible-pointer-types]
  461 |                         c = (*seq)->center;
      |                           ^
sumaclust.c: In function ‘putSeqInCluster’:
sumaclust.c:583:24: error: assignment to ‘struct fastaSeqPtr *’ from incompatible pointer type ‘struct <anonymous> **’ [-Wincompatible-pointer-types]
  583 |         (*seq)->center = center;
      |                        ^
sumaclust.c: In function ‘computeClusterWeights’:
sumaclust.c:750:24: error: assignment to ‘struct <anonymous> **’ from incompatible pointer type ‘struct fastaSeqPtr *’ [-Wincompatible-pointer-types]
  750 |                 center = (*seq)->center;
      |                        ^
sumaclust.c:763:24: error: assignment to ‘struct <anonymous> **’ from incompatible pointer type ‘struct fastaSeqPtr *’ [-Wincompatible-pointer-types]
  763 |                 center = (*seq)->center;
      |                        ^
sumaclust.c: In function ‘main’:
sumaclust.c:1001:42: error: assignment to ‘struct fastaSeqPtr *’ from incompatible pointer type ‘fastaSeqPtr’ {aka ‘struct <anonymous> *’} [-Wincompatible-pointer-types]
 1001 |                 ((db.fastaSeqs)+i)->next = (db.fastaSeqs)+i-1;
      |                                          ^
sumaclust.c:1009:73: error: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types]
 1009 |                         qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), sortSeqsWithCounts);
      |                                                                         ^~~~~~~~~~~~~~~~~~
      |                                                                         |
      |                                                                         int (*)(const void **, const void **)
In file included from sumaclust.c:9:
/usr/include/stdlib.h:971:34: note: expected ‘__compar_fn_t’ {aka ‘int (*)(const void *, const void *)’} but argument is of type ‘int (*)(const void **, const void **)’
  971 |                    __compar_fn_t __compar) __nonnull ((1, 4));
      |                    ~~~~~~~~~~~~~~^~~~~~~~
sumaclust.c:1011:73: error: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types]
 1011 |                         qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), reverseSortSeqsWithCounts);
      |                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                         |
      |                                                                         int (*)(const void **, const void **)
/usr/include/stdlib.h:971:34: note: expected ‘__compar_fn_t’ {aka ‘int (*)(const void *, const void *)’} but argument is of type ‘int (*)(const void **, const void **)’
  971 |                    __compar_fn_t __compar) __nonnull ((1, 4));
      |                    ~~~~~~~~~~~~~~^~~~~~~~
sumaclust.c:1017:73: error: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types]
 1017 |                         qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), sortSeqsP);
      |                                                                         ^~~~~~~~~
      |                                                                         |
      |                                                                         int (*)(const void **, const void **)
/usr/include/stdlib.h:971:34: note: expected ‘__compar_fn_t’ {aka ‘int (*)(const void *, const void *)’} but argument is of type ‘int (*)(const void **, const void **)’
  971 |                    __compar_fn_t __compar) __nonnull ((1, 4));
      |                    ~~~~~~~~~~~~~~^~~~~~~~
sumaclust.c:1019:73: error: passing argument 4 of ‘qsort’ from incompatible pointer type [-Wincompatible-pointer-types]
 1019 |                         qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), reverseSortSeqsP);
      |                                                                         ^~~~~~~~~~~~~~~~
      |                                                                         |
      |                                                                         int (*)(const void **, const void **)
/usr/include/stdlib.h:971:34: note: expected ‘__compar_fn_t’ {aka ‘int (*)(const void *, const void *)’} but argument is of type ‘int (*)(const void **, const void **)’
  971 |                    __compar_fn_t __compar) __nonnull ((1, 4));
      |                    ~~~~~~~~~~~~~~^~~~~~~~
sumaclust.c:1049:61: error: passing argument 2 of ‘printSeq’ from incompatible pointer type [-Wincompatible-pointer-types]
 1049 |                         printSeq(uniqSeqs+i, (*(uniqSeqs+i))->center, (*(uniqSeqs+i))->score, FASTA_output);
      |                                              ~~~~~~~~~~~~~~~^~~~~~~~
      |                                                             |
      |                                                             struct fastaSeqPtr *
sumaclust.c:512:46: note: expected ‘struct <anonymous> **’ but argument is of type ‘struct fastaSeqPtr *’
  512 | void printSeq(fastaSeqPtr* seq, fastaSeqPtr* center, double score, FILE* output)
      |                                 ~~~~~~~~~~~~~^~~~~~
make[1]: *** [global.mk:20: sumaclust.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2