Your message dated Sun, 25 Aug 2024 13:50:55 +0000
with message-id <e1siddv-000fmc...@fasolo.debian.org>
and subject line Bug#1075198: fixed in libpsortb 1.0+dfsg-7
has caused the Debian Bug report #1075198,
regarding libpsortb: ftbfs with GCC-14
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.
(NB: If you are a system administrator and have no idea what this
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--
1075198: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075198
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:libpsortb
Version: 1.0+dfsg-6
Severity: important
Tags: sid trixie
User: debian-...@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/libpsortb_1.0+dfsg-6_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
[...]
| ^~~~~~~~~~~~~~~~~~~~~~~~
readseqs_multialpha.c:874:9: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
874 | fgets(line, MAX_LINE, seqfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hmmsearch.c:712:44: warning: format ‘%s’ expects argument of type ‘char *’, but
argument 2 has type ‘struct letter_s *’ [-Wformat=]
712 | printf("Could not find letter %s when scoring null
model\n", &seq[l]);
| ~^
~~~~~~~
| |
|
| char *
struct letter_s *
readseqs_multialpha.c:995:9: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
995 | fgets(line, MAX_LINE, seqfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
std_funcs.c:2452:5: note: declared here
2452 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di,
struct hmm_multi_s *hmmp,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c: In function ‘read_module_multi’:
readhmm_multialpha.c:1039:5: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1039 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1074:5: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1074 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm.c: In function ‘read_prior_files’:
readhmm_multialpha.c:1108:5: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1108 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm.c:1225:5: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
1225 | fgets(ps, 2048, priorfile);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1137:5: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1137 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1140:7: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1140 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1166:7: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1166 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1169:7: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1169 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1195:7: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1195 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
readhmm_multialpha.c:1199:7: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1199 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:479: readhmm.lo] Error 1
readhmm_multialpha.c:1226:7: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1226 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** Waiting for unfinished jobs....
readhmm_multialpha.c:1233:3: warning: ignoring return value of ‘fgets’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
1233 | fgets(s, MAX_LINE, file);
| ^~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:479: readseqs_multialpha.lo] Error 1
make[3]: *** [Makefile:479: readhmm_multialpha.lo] Error 1
make[3]: *** [Makefile:479: hmmsearch.lo] Error 1
make[3]: *** [Makefile:479: std_funcs.lo] Error 1
make[3]: *** [Makefile:479: core_algorithms_multialpha.lo] Error 1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
debug_funcs.c -o debug_funcs.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/modhmm0.92b'
make[2]: *** [Makefile:408: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:340: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libpsortb
Source-Version: 1.0+dfsg-7
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
libpsortb, 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 1075...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated libpsortb 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 25 Aug 2024 15:12:08 +0200
Source: libpsortb
Architecture: source
Version: 1.0+dfsg-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075198
Changes:
libpsortb (1.0+dfsg-7) unstable; urgency=medium
.
* gcc14.patch: new: fix multiple issues caught by gcc14. (Closes: #1075198)
* d/control: add myself to uploaders.
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Files:
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