[Debian-med-packaging] Bug#1097649: primer3: ftbfs with GCC-15

[Matthias Klose]

Package: src:primer3
Version: 2.6.1-5
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/primer3_2.6.1-5_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

[...]
  888 |   if ((pa->pick_left_primer) && ((&retval->fwd) != NULL )
      |                                                 ^~
libprimer3.h:927:15: note: ‘fwd’ declared here
  927 |   oligo_array fwd, intl, rev;
      |               ^~~
format_output.c:907:53: warning: the comparison will always evaluate as ‘true’ for the address of ‘intl’ will never be NULL [-Waddress]
  907 |   if ((pa->pick_internal_oligo) && ((&retval->intl) != NULL )
      |                                                     ^~
libprimer3.h:927:20: note: ‘intl’ declared here
  927 |   oligo_array fwd, intl, rev;
      |                    ^~~~
format_output.c:926:50: warning: the comparison will always evaluate as ‘true’ for the address of ‘rev’ will never be NULL [-Waddress]
  926 |   if ((pa->pick_right_primer) && ((&retval->rev) != NULL )
      |                                                  ^~
libprimer3.h:927:26: note: ‘rev’ declared here
  927 |   oligo_array fwd, intl, rev;
      |                          ^~~
read_boulder.c:106:15: error: conflicting types for ‘strtod’; have ‘double(void)’
  106 | extern double strtod();
      |               ^~~~~~
In file included from read_boulder.c:45:
/usr/include/stdlib.h:118:15: note: previous declaration of ‘strtod’ with type ‘double(const char * restrict,  char ** restrict)’
  118 | extern double strtod (const char *__restrict __nptr,
      |               ^~~~~~
read_boulder.c: In function ‘parse_double’:
read_boulder.c:1001:12: error: too many arguments to function ‘strtod’; expected 0, have 2
 1001 |     *out = strtod(datum, &nptr);
      |            ^~~~~~ ~~~~~
read_boulder.c:106:15: note: declared here
  106 | extern double strtod();
      |               ^~~~~~
make[2]: *** [Makefile:225: read_boulder.o] Error 1
make[2]: *** Waiting for unfinished jobs....
libprimer3.cc: In function ‘char* strstr_nocase(char*, char*)’:
libprimer3.cc:6168:29: warning: pointer ‘p’ used after ‘void free(void*)’ [-Wuse-after-free]
 6168 |     else {free(tmp); return p;}
      |                             ^
libprimer3.cc:6168:15: note: call to ‘void free(void*)’ here
 6168 |     else {free(tmp); return p;}
      |           ~~~~^~~~~
In file included from /usr/include/string.h:548,
                 from thal.c:43:
In function ‘strcpy’,
    inlined from ‘safe_malloc’ at thal.c:804:7,
    inlined from ‘calc_hairpin’ at thal.c:1922:19:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
   81 |   return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’
In function ‘strcpy’,
    inlined from ‘safe_malloc’ at thal.c:804:7,
    inlined from ‘calc_bulge_internal.isra’ at thal.c:2000:19:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
   81 |   return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’
In function ‘strcpy’,
    inlined from ‘safe_malloc’ at thal.c:804:7,
    inlined from ‘maxTM’ at thal.c:1542:19,
    inlined from ‘fillMatrix’ at thal.c:1473:16:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected [-Wnonnull]
   81 |   return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’
make[2]: Leaving directory '/build/reproducible-path/primer3-2.6.1/src'
dh_auto_build: error: cd src && make -j8 "INSTALL=install --strip-program=true" CPP=\$\(CXX\) returned exit code 2
make[1]: *** [debian/rules:20: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/primer3-2.6.1'
make: *** [debian/rules:17: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2