Your message dated Mon, 06 Oct 2025 21:09:11 +0000
with message-id <[email protected]>
and subject line Bug#1097649: fixed in primer3 2.6.1-6
has caused the Debian Bug report #1097649,
regarding primer3: ftbfs with GCC-15
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1097649: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097649
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:primer3
Version: 2.6.1-5
Severity: important
Tags: sid forky
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: primer3
Source-Version: 2.6.1-6
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
primer3, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated primer3 package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 06 Oct 2025 22:24:23 +0200
Source: primer3
Architecture: source
Version: 2.6.1-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097649
Changes:
primer3 (2.6.1-6) unstable; urgency=medium
.
* Team upload.
* gcc15.patch: new: remove SunOS workaround.
This allows fixing a build failure with gcc-15. (Closes: #1097649)
* d/copyright: remove the old fsf address.
* d/watch: convert to v5 github template.
* d/control: declare compliance to standards version 4.7.2.
* d/control: drop redundant Rules-Requires-Root: no.
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Files:
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