[Debian-med-packaging] Bug#1097647: prime-phylo: ftbfs with GCC-15

[Matthias Klose]

Package: src:prime-phylo
Version: 1.0.11-13
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/prime-phylo_1.0.11-13_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

[...]
      | ^~~~~~~~~~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_set_definition’:
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:327:1: warning: old-style function definition [-Wold-style-definition]
  327 | seq_set_definition(e, s)
      | ^~~~~~~~~~~~~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_set_accession’:
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:352:1: warning: old-style function definition [-Wold-style-definition]
  352 | seq_set_accession(e, s)
      | ^~~~~~~~~~~~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_free_comments’:
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:369:1: warning: old-style function definition [-Wold-style-definition]
  369 | seq_free_comments(c)
      | ^~~~~~~~~~~~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_free’:
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:383:1: warning: old-style function definition [-Wold-style-definition]
  383 | seq_free(entries)
      | ^~~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function ‘yyparse’:
/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1391:7: error: too many arguments to function ‘yyerror’; expected 0, have 1
 1391 |       yyerror (YY_("syntax error"));
      |       ^~~~~~~
gb.y:28:12: note: declared here
/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1502:3: error: too many arguments to function ‘yyerror’; expected 0, have 1
 1502 |   yyerror (YY_("memory exhausted"));
      |   ^~~~~~~
gb.y:28:12: note: declared here
gb.y: At top level:
gb.y:291:1: error: conflicting types for ‘yyerror’; have ‘int(char *)’
gb.y:28:12: note: previous declaration of ‘yyerror’ with type ‘int(void)’
gb.y:310:1: error: conflicting types for ‘new_entry’; have ‘struct entry *(char *, struct string_part *)’
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/entry.h:151:21: note: previous declaration of ‘new_entry’ with type ‘struct entry *(void)’
  151 | struct entry       *new_entry();
      |                     ^~~~~~~~~
gb.y: In function ‘add_to_seq’:
gb.y:399:1: warning: old-style function definition [-Wold-style-definition]
gb.y:403:9: warning: unused variable ‘new_buf’ [-Wunused-variable]
gb.y: At top level:
gb.y:28:12: warning: ‘yyerror’ used but never defined
make[3]: *** [src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make:136: src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o] Error 1
make[3]: *** Waiting for unfinished jobs....
seqreader.l: In function ‘seq_read’:
seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable]
/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level:
/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function]
 1864 |     static int input  (void)
      |                ^~~~~
/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: ‘yyunput’ defined but not used [-Wunused-function]
 1821 |     static void yyunput (int c, char * yy_bp )
      |                 ^~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’:
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=]
  303 |                 tmp->text = strdup(s);
      |                    ^~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’
  301 |             tmp = (struct comment *) malloc(sizeof(struct comment *));
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:304:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=]
  304 |                 tmp->next = NULL;
      |                    ^~
/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’
  301 |             tmp = (struct comment *) malloc(sizeof(struct comment *));
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:413: src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/all] Error 2
make[2]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2