[Debian-med-packaging] Bug#1075359: paml: ftbfs with GCC-14

[Matthias Klose]

Package: src:paml
Version: 4.9j+dfsg-4
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/paml_4.9j+dfsg-4_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

[...]
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
codeml.c:4052:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 4052 |             fscanf(fin, "%d", &j);
      |             ^~~~~~~~~~~~~~~~~~~~~
codeml.c:4056:13: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 4056 |             fgets(line, nline, fin);
      |             ^~~~~~~~~~~~~~~~~~~~~~~
codeml.c: In function ‘PairwiseCodon’:
codeml.c:4318:13: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 4318 |             scanf("%d%d", &is, &js);
      |             ^~~~~~~~~~~~~~~~~~~~~~~
codeml.c: In function ‘lfunNSsites_rate’:
codeml.c:5238:10: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5238 |          scanf("%d", &continuous);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~
codeml.c:5251:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5251 |             fscanf(fsites, "%d%s", &it, sitelabel);
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘scanfile’:
tools.c:5356:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5356 |       fgets(line, lline, fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘DescriptiveStatistics’:
tools.c:5678:10: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5678 |          fscanf(fin, "%lf", &data[j*n + i]);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools.c:5689:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5689 |       scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘gfopen’:
tools.c:1148:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1148 |       scanf("%s", filename);
      |       ^~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘scanfile’:
tools.c:5356:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5356 |       fgets(line, lline, fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘DescriptiveStatistics’:
tools.c:5678:10: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5678 |          fscanf(fin, "%lf", &data[j*n + i]);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools.c:5689:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5689 |       scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘gfopen’:
tools.c:1148:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1148 |       scanf("%s", filename);
      |       ^~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘scanfile’:
tools.c:5356:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5356 |       fgets(line, lline, fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~
tools.c: In function ‘DescriptiveStatistics’:
tools.c:5678:10: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5678 |          fscanf(fin, "%lf", &data[j*n + i]);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tools.c:5689:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 5689 |       scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[1]: *** [Makefile:14: basemlg] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [Makefile:20: pamp] Error 1
make[1]: *** [Makefile:12: baseml] Error 1
make[1]: *** [Makefile:16: codeml] Error 1
make[1]: *** [Makefile:25: yn00] Error 1
make[1]: *** [Makefile:22: mcmctree] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:13: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2