[Debian-med-packaging] Bug#1097779: readseq: ftbfs with GCC-15

[Matthias Klose]

Package: src:readseq
Version: 1-15
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/readseq_1-15_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

[...]
 1972 |       fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
      |                          ~^                                  ~~~~~~
      |                           |                                  |
      |                           int                                long int
      |                          %ld
ureadseq.c:1972:37: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=]
 1972 |       fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
      |                                    ~^                                ~~~~~~~~
      |                                     |                                |
      |                                     unsigned int                     long unsigned int
      |                                    %lX
ureadseq.c:1979:25: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
 1979 |         fprintf(outf,"%4d %-60s\n",seqlen,seqname);
      |                       ~~^          ~~~~~~
      |                         |          |
      |                         int        long int
      |                       %4ld
ureadseq.c:2002:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=]
 2002 |       fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
      |                          ~^                                  ~~~~~~
      |                           |                                  |
      |                           int                                long int
      |                          %ld
ureadseq.c:2002:37: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=]
 2002 |       fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
      |                                    ~^                                ~~~~~~~~
      |                                     |                                |
      |                                     unsigned int                     long unsigned int
      |                                    %lX
ureadseq.c:2043:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
 2043 |         if (numline==1) fprintf(outf,"%-9d ",i+1);
      |                                       ~~~^   ~~~
      |                                          |    |
      |                                          int  long int
      |                                       %-9ld
ureadasn.c: In function ‘listASNSeqs’:
ureadasn.c:189:24: warning: passing argument 1 of ‘AsnIoOpen’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  189 |   if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit;
      |                        ^~~~~~~~
In file included from /usr/include/ncbi/ncbi.h:57,
                 from ureadasn.c:13:
/usr/include/ncbi/asn.h:384:54: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but argument is of type ‘const char *’
  384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode));
/usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’
  192 | #define PROTO(x) x      /* Prototypes are acceptable */
      |                  ^
ureadasn.c: In function ‘readASNSeq’:
ureadasn.c:261:24: warning: passing argument 1 of ‘AsnIoOpen’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  261 |   if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit;
      |                        ^~~~~~~~
/usr/include/ncbi/asn.h:384:54: note: expected ‘Nlm_CharPtr’ {aka ‘char *’} but argument is of type ‘const char *’
  384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode));
/usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro ‘PROTO’
  192 | #define PROTO(x) x      /* Prototypes are acceptable */
      |                  ^
ureadasn.c:262:31: warning: ‘fgets’ writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=]
  262 |   for (i=0; i<skiplines; i++) fgets( stemp, 255, aip->fp);  /* this may mess up asn routines... */
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~
ureadasn.c:241:15: note: destination object ‘stemp’ of size 200
  241 |   char  *seq, stemp[200];
      |               ^~~~~
In file included from ureadasn.c:8:
/usr/include/stdio.h:654:14: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’
  654 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
      |              ^~~~~
make[1]: *** [Makefile:51: build] Error 1
make[1]: Leaving directory '/build/reproducible-path/readseq-1'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2