Control: forwarded -1 Céline Mercier <celine.merc...@metabarcoding.org>
Control: tags -1 upstream
Thanks
Hi Céline,
the Debian packaged sumaclust fails to build from source when trying to
build with GCC 14. It would be great if you could fix the errors
mentioned below.
Kind regards
Andreas.
----- Weitergeleitete Nachricht von Matthias Klose <d...@debian.org> -----
Date: Wed, 03 Jul 2024 12:45:09 +0000
From: Matthias Klose <d...@debian.org>
To: mainto...@bugs.debian.org
Subject: sumaclust: ftbfs with GCC-14
Package: src:sumaclust
Version: 1.0.36+ds-2
Severity: important
Tags: sid trixie
User: debian-...@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
----- Ende weitergeleitete Nachricht -----
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