[Debian-med-packaging] Bug#1075419: python-pairix: ftbfs with GCC-14

[Matthias Klose]

Package: src:python-pairix
Version: 0.3.7-7
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/python-pairix_0.3.7-7_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

[...]
 1246 |          char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
      |                               ^~~~~~~~~~
src/index.c:1263:59: error: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
 1263 |          sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
      |                                                           ^~~~~~~
      |                                                           |
      |                                                           char **
src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’
  131 |         sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
      |                                                            ~~~~~~~~~~~~~^~~~
src/index.c: In function ‘ti_query_2d_tid’:
src/index.c:1417:31: error: returning ‘ti_iter_t’ {aka ‘struct __ti_iter_t *’} from a function with return type ‘int’ makes integer from pointer without a cast [-Wint-conversion]
 1417 |         if (name == 0) return ti_iter_first();
      |                               ^~~~~~~~~~~~~~~
src/index.c: In function ‘create_merged_iter’:
src/index.c:1469:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 1469 |      if( miter->iu = calloc(n,sizeof(iter_unit*))) {
      |          ^~~~~
src/index.c: In function ‘merged_ti_read’:
src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1537 |         miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly);
      |                   ^
src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1543 |       miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter
      |                 ^
src/index.c: In function ‘sequential_ti_read’:
src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1573 |     char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
      |               ^~~~~~~~~~~~
src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1576 |       s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
      |         ^
src/index.c: In function ‘get_unique_merged_seqname’:
src/index.c:1643:22: error: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
 1643 |             seqnames = ti_seqname(tbs[i]->idx,&len);
      |                      ^
src/index.c: In function ‘flip_region’:
src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable]
 1744 |     int l, i, l2, split_pos;
      |                   ^~~~~~~~~
src/index.c: In function ‘querys_2D_wrapper’:
src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1911 |         char *reg2 = flip_region(reg, get_region_split_character(tb));
      |                                  ^~~
src/index.c:1743:27: note: expected ‘char *’ but argument is of type ‘const char *’
 1743 | char *flip_region ( char* s, char region_split_character) {
      |                     ~~~~~~^
src/index.c: In function ‘check_triangle’:
src/index.c:1971:23: error: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
 1971 |     char **seqnames = ti_seqname(idx,&len);
      |                       ^~~~~~~~~~
src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1977 |           if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); }  // not a triangle
      |                                                                ^~~~
In file included from src/khash.h:94,
                 from src/index.c:4:
/usr/include/stdlib.h:687:25: note: expected ‘void *’ but argument is of type ‘const char *’
  687 | extern void free (void *__ptr) __THROW;
      |                   ~~~~~~^~~~~
src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1978 |         free(reg2);
      |              ^~~~
/usr/include/stdlib.h:687:25: note: expected ‘void *’ but argument is of type ‘const char *’
  687 | extern void free (void *__ptr) __THROW;
      |                   ~~~~~~^~~~~
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build 
dh_auto_build: error: pybuild --build -i python{version} -p "3.11 3.12" returned exit code 13
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2