[Debian-med-packaging] Bug#1097956: sweed: ftbfs with GCC-15

[Matthias Klose]

Package: src:sweed
Version: 3.2.1+dfsg-6
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
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