Your message dated Fri, 13 Dec 2024 13:20:02 +0000
with message-id <[email protected]>
and subject line Bug#1075545: fixed in sumaclust 1.0.36+ds-3
has caused the Debian Bug report #1075545,
regarding sumaclust: ftbfs with GCC-14
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1075545: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075545
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:sumaclust
Version: 1.0.36+ds-2
Severity: important
Tags: sid trixie
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: sumaclust
Source-Version: 1.0.36+ds-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sumaclust, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated sumaclust package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
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Hash: SHA512
Format: 1.8
Date: Fri, 13 Dec 2024 14:02:56 +0100
Source: sumaclust
Architecture: source
Version: 1.0.36+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1075545
Changes:
sumaclust (1.0.36+ds-3) unstable; urgency=medium
.
* Remove Tim Booth <[email protected]> since address is bouncing
(Thank you for your work on this package, Tim)
* Use -Wno-incompatible-pointer-types to build with gcc-14
Closes: #1075545
* Standards-Version: 4.7.0 (routine-update)
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