Your message dated Sat, 25 Oct 2025 12:54:10 +0000
with message-id <[email protected]>
and subject line Bug#1097956: fixed in sweed 3.2.1+dfsg-7
has caused the Debian Bug report #1097956,
regarding sweed: ftbfs with GCC-15
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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--
1097956: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097956
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:sweed
Version: 3.2.1+dfsg-6
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/sweed_3.2.1+dfsg-6_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html
[...]
SweeD_BFGS.c:1643:33: error: prototype declaration
1643 | extern /* Subroutine */ int dscal_();
| ^~~~~~
SweeD_BFGS.c: In function ‘dtrsl_’:
SweeD_BFGS.c:4125:33: warning: old-style function definition
[-Wold-style-definition]
4125 | extern /* Subroutine */ int dtrsl_();
| ^~~~~~
SweeD_BFGS.c:5755:1: error: number of arguments doesn’t match prototype
5755 | {
| ^
SweeD_BFGS.c:4125:33: error: prototype declaration
4125 | extern /* Subroutine */ int dtrsl_();
| ^~~~~~
SweeD_BFGS.c:5873:9: error: too many arguments to function ‘daxpy_’; expected
0, have 6
5873 | daxpy_(&i__2, &temp, &t[j + (j - 1) * t_dim1], &c__1, &b[j],
&c__1);
| ^~~~~~ ~~~~~
SweeD_BFGS.c:1648:43: note: declared here
1648 | extern /* Subroutine */ int dcopy_(), daxpy_();
| ^~~~~~
SweeD_BFGS.c:5891:9: error: too many arguments to function ‘daxpy_’; expected
0, have 6
5891 | daxpy_(&j, &temp, &t[(j + 1) * t_dim1 + 1], &c__1, &b[1],
&c__1);
| ^~~~~~ ~~
SweeD_BFGS.c:1648:43: note: declared here
1648 | extern /* Subroutine */ int dcopy_(), daxpy_();
| ^~~~~~
SweeD_BFGS.c:5909:17: error: too many arguments to function ‘ddot_’; expected
0, have 5
5909 | b[j] -= ddot_(&i__2, &t[j + 1 + j * t_dim1], &c__1, &b[j + 1],
&c__1);
| ^~~~~ ~~~~~
SweeD_BFGS.c:3333:23: note: declared here
3333 | extern doublereal ddot_();
| ^~~~~
SweeD_BFGS.c:5926:17: error: too many arguments to function ‘ddot_’; expected
0, have 5
5926 | b[j] -= ddot_(&i__2, &t[j * t_dim1 + 1], &c__1, &b[1], &c__1);
| ^~~~~ ~~~~~
SweeD_BFGS.c:3333:23: note: declared here
3333 | extern doublereal ddot_();
| ^~~~~
make[2]: *** [Makefile.gcc:35: SweeD_BFGS.o] Error 1
make[2]: *** Waiting for unfinished jobs....
SweeD.c: In function ‘main’:
SweeD.c:316:9: warning: ‘strncat’ output may be truncated copying <unknown>
bytes from a string of length 999 [-Wstringop-truncation]
316 |
strncat(infoFileName,runName,INFILENAMESIZE-strlen(infoFileName));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SweeD.c:320:9: warning: ‘strncat’ output may be truncated copying <unknown>
bytes from a string of length 999 [-Wstringop-truncation]
320 |
strncat(warnFileName,runName,INFILENAMESIZE-strlen(warnFileName));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SweeD.c:324:9: warning: ‘strncat’ output may be truncated copying <unknown>
bytes from a string of length 999 [-Wstringop-truncation]
324 |
strncat(clrReportFileName,runName,INFILENAMESIZE-strlen(clrReportFileName));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SweeD_Kernel.c: In function ‘getAlpha’:
SweeD_Kernel.c:383:26: warning: ‘lik’ may be used uninitialized
[-Wmaybe-uninitialized]
383 | *likelihood = lik[maxPos];
| ~~~^~~~~~~~
SweeD_Kernel.c:340:15: note: ‘lik’ declared here
340 | t_sfs lik[LOCALGRIDSIZE];
| ^~~
SweeD_Input.c: In function ‘findFirstAlignment’:
SweeD_Input.c:1009:17: warning: ‘strncpy’ specified bound 100 equals
destination size [-Wstringop-truncation]
1009 | strncpy(VCF_alignment_name, *string,
MAX_CHROM_NAME_VCF);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SweeD_Input.c: In function ‘readLine_VCF’:
SweeD_Input.c:2672:41: warning: ‘strncpy’ specified bound 100 equals
destination size [-Wstringop-truncation]
2672 | strncpy(VCF_alignment_name,
*string, MAX_CHROM_NAME_VCF);
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/build/reproducible-path/sweed-3.2.1+dfsg'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" -f
Makefile.gcc returned exit code 2
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/sweed-3.2.1+dfsg'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: sweed
Source-Version: 3.2.1+dfsg-7
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sweed, 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.
Santiago Vila <[email protected]> (supplier of updated sweed 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])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 25 Oct 2025 14:10:00 +0200
Source: sweed
Architecture: source
Version: 3.2.1+dfsg-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1097956
Changes:
sweed (3.2.1+dfsg-7) unstable; urgency=medium
.
* Team upload.
.
[ Adrian Bunk ]
* Build with -std=gnu17 to workaround FTBFS with GCC 15.
Closes: #1097956.
.
[ Santiago Vila ]
* d/control: Drop "Rules-Requires-Root: no" (default).
* d/control: Update standards-version.
* d/salsa-ci.yml: Allow blhc to fail.
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