Your message dated Mon, 22 Sep 2025 20:40:01 +0000
with message-id <[email protected]>
and subject line Bug#1097647: fixed in prime-phylo 1.0.11-14
has caused the Debian Bug report #1097647,
regarding prime-phylo: 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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--
1097647: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097647
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:prime-phylo
Version: 1.0.11-13
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/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
--- End Message ---
--- Begin Message ---
Source: prime-phylo
Source-Version: 1.0.11-14
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
prime-phylo, 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 prime-phylo 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, 22 Sep 2025 21:44:48 +0200
Source: prime-phylo
Architecture: source
Version: 1.0.11-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097647 1113421
Changes:
prime-phylo (1.0.11-14) unstable; urgency=medium
.
* gcc-15.patch: new: fix build failures with gcc-15. (Closes: #1097647)
* cmake-4.patch: new: fix build failure past cmake 4. (Closes: #1113421)
* d/watch: convert to v5 untrackable upstream.
* d/control: R³ now defaults to no, thus redundant.
* d/patches/*: normalize Last-Update timestamp.
* d/control: declare compliance to standards version 4.7.2.
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prime-phylo_1.0.11-14.debian.tar.xz
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Files:
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prime-phylo_1.0.11-14.debian.tar.xz
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