Your message dated Sun, 13 Aug 2023 10:04:13 +0000
with message-id <e1qv7xf-000ct6...@fasolo.debian.org>
and subject line Bug#1037689: fixed in hhsuite 3.3.0+ds-8
has caused the Debian Bug report #1037689,
regarding hhsuite: ftbfs with GCC-13
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1037689: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037689
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:hhsuite
Version: 3.3.0+ds-7
Severity: normal
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-13

[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-13/g++-13, but succeeds to build with gcc-12/g++-12. 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/2023/05/22/logs/hhsuite_3.3.0+ds-7_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html

[...]
[  9%] Linking C static library libffindex.a
cd /<<PKGBUILDDIR>>/build_plain/lib/ffindex/src && /usr/bin/cmake -P 
CMakeFiles/ffindex.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build_plain/lib/ffindex/src && /usr/bin/cmake -E 
cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1
make[4]: *** [src/CMakeFiles/A3M_COMPRESS.dir/build.make:79: 
src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
make[3]: *** [CMakeFiles/Makefile2:843: src/CMakeFiles/A3M_COMPRESS.dir/all] 
Error 2
make[3]: *** Waiting for unfinished jobs....
/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o 
CMakeFiles/ffindex.dir/ffutil.c.o
[ 10%] Generating ../generated/cs219.lib.h
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/build_plain/generated
cd /<<PKGBUILDDIR>>/data && /<<PKGBUILDDIR>>/cmake/xxdi.pl cs219.lib > 
/<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h
/usr/bin/ranlib libffindex.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
[ 10%] Built target ffindex
[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP 
-I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src 
-I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde 
-I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse 
-fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o 
-MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c 
/<<PKGBUILDDIR>>/src/cs/as.cc
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned 
char!' < /<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h > 
/<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f 
/<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h.tmp 
/<<PKGBUILDDIR>>/build_plain/generated/cs219.lib.h
[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP 
-I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src 
-I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde 
-I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse 
-fopenmp -fno-strict-aliasing -MD -MT 
src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF 
CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o 
CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c 
/<<PKGBUILDDIR>>/src/cs/assert_helpers.cc
[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP 
-I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src 
-I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde 
-I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse 
-fopenmp -fno-strict-aliasing -MD -MT 
src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF 
CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o 
CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c 
/<<PKGBUILDDIR>>/src/cs/blosum_matrix.cc
[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP 
-I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src 
-I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde 
-I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse 
-fopenmp -fno-strict-aliasing -MD -MT 
src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF 
CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o 
CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /<<PKGBUILDDIR>>/src/cs/getopt_pp.cc
[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP 
-I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src 
-I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde 
-I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse 
-fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o 
-MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o 
-c /<<PKGBUILDDIR>>/src/cs/log.cc
[ 16%] Linking CXX static library libhhviterbialgorithm_and_ss.a
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -P 
CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -E cmake_link_script 
CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_and_ss.a 
CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
[ 16%] Built target hhviterbialgorithm_and_ss
[ 17%] Linking CXX static library libhhviterbialgorithm_with_celloff.a
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -P 
CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake
[ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/c++ -DOPENMP 
-I/<<PKGBUILDDIR>>/build_plain/generated -I/<<PKGBUILDDIR>>/src 
-I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde 
-I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/build_plain/src -g -O2 
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat 
-Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 
-O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse 
-fopenmp -fno-strict-aliasing -MD -MT 
src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF 
CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o 
CMakeFiles/CS_OBJECTS.dir/application.cc.o -c 
/<<PKGBUILDDIR>>/src/cs/application.cc
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -E cmake_link_script 
CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a 
CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
[ 19%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a
/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -P 
CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
cd /<<PKGBUILDDIR>>/build_plain/src && /usr/bin/cmake -E cmake_link_script 
CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1
[ 19%] Built target hhviterbialgorithm_with_celloff
/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a 
CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
[ 19%] Built target hhviterbialgorithm_with_celloff_and_ss
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned 
char!' < /<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h > 
/<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h.tmp
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned 
char!' < /<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h > 
/<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f 
/<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h.tmp 
/<<PKGBUILDDIR>>/build_plain/generated/context_data.lib.h
[ 20%] Linking CXX static library libCS_OBJECTS.a
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/cmake -P 
CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build_plain/src/cs && /usr/bin/cmake -E cmake_link_script 
CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1
/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o 
CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o 
CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o 
CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o 
CMakeFiles/CS_OBJECTS.dir/application.cc.o
/usr/bin/ranlib libCS_OBJECTS.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
cd /<<PKGBUILDDIR>>/data && mv -f 
/<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h.tmp 
/<<PKGBUILDDIR>>/build_plain/generated/context_data.crf.h
[ 20%] Built target CS_OBJECTS
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
[ 20%] Built target generated
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
make[2]: *** [Makefile:159: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build_plain'
dh_auto_build: error: cd build_plain && make -j8 "INSTALL=install 
--strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:67: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:134: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

--- End Message ---
--- Begin Message ---
Source: hhsuite
Source-Version: 3.3.0+ds-8
Done: Étienne Mollier <emoll...@debian.org>

We believe that the bug you reported is fixed in the latest version of
hhsuite, 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 1037...@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 hhsuite 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, 13 Aug 2023 10:47:11 +0200
Source: hhsuite
Architecture: source
Version: 3.3.0+ds-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1037689
Changes:
 hhsuite (3.3.0+ds-8) unstable; urgency=medium
 .
   * Team upload.
   * gcc-13.patch: new: fix ftbfs with gcc 13. (Closes: #1037689)
   * d/control: declare compliance to standards version 4.6.2.
Checksums-Sha1:
 0afe788e3ebb3736c61225b38457a98e57a320b2 2271 hhsuite_3.3.0+ds-8.dsc
 0c6aa80d717ee79df31a05f33d2f461b1b6f0c88 16868 hhsuite_3.3.0+ds-8.debian.tar.xz
Checksums-Sha256:
 61afd54c119d7bf8d60ffee1a9b5151f8c1bb20943a2f72671c8aa0ae4680171 2271 
hhsuite_3.3.0+ds-8.dsc
 d408a3d42581737068f06b96cd922c462f672beeb4faf94f41ac37340170b3cb 16868 
hhsuite_3.3.0+ds-8.debian.tar.xz
Files:
 2e8a40e3a6d16147e1c27e1053b95b77 2271 science optional hhsuite_3.3.0+ds-8.dsc
 81b05abfd099550bfb153063e218961e 16868 science optional 
hhsuite_3.3.0+ds-8.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=vOej
-----END PGP SIGNATURE-----

--- End Message ---

Reply via email to