[Debian-med-packaging] Bug#1075198: libpsortb: ftbfs with GCC-14

[Matthias Klose]

Package: src:libpsortb
Version: 1.0+dfsg-6
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/libpsortb_1.0+dfsg-6_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

[...]
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
readseqs_multialpha.c:874:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  874 |         fgets(line, MAX_LINE, seqfile);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmsearch.c:712:44: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘struct letter_s *’ [-Wformat=]
  712 |             printf("Could not find letter %s when scoring null model\n", &seq[l]);
      |                                           ~^                             ~~~~~~~
      |                                            |                             |
      |                                            char *                        struct letter_s *
readseqs_multialpha.c:995:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  995 |         fgets(line, MAX_LINE, seqfile);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
std_funcs.c:2452:5: note: declared here
 2452 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c: In function ‘read_module_multi’:
readhmm_multialpha.c:1039:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1039 |     fgets(s, MAX_LINE, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1074:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1074 |     fgets(s, MAX_LINE, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm.c: In function ‘read_prior_files’:
readhmm_multialpha.c:1108:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1108 |     fgets(s, MAX_LINE, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm.c:1225:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1225 |     fgets(ps, 2048, priorfile);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1137:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1137 |     fgets(s, MAX_LINE, file);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1140:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1140 |       fgets(s, MAX_LINE, file);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1166:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1166 |       fgets(s, MAX_LINE, file);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1169:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1169 |       fgets(s, MAX_LINE, file);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1195:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1195 |       fgets(s, MAX_LINE, file);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1199:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1199 |       fgets(s, MAX_LINE, file);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:479: readhmm.lo] Error 1
readhmm_multialpha.c:1226:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1226 |       fgets(s, MAX_LINE, file);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** Waiting for unfinished jobs....
readhmm_multialpha.c:1233:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1233 |   fgets(s, MAX_LINE, file);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:479: readseqs_multialpha.lo] Error 1
make[3]: *** [Makefile:479: readhmm_multialpha.lo] Error 1
make[3]: *** [Makefile:479: hmmsearch.lo] Error 1
make[3]: *** [Makefile:479: std_funcs.lo] Error 1
make[3]: *** [Makefile:479: core_algorithms_multialpha.lo] Error 1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/modhmm0.92b'
make[2]: *** [Makefile:408: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:340: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2