Your message dated Wed, 09 Aug 2023 16:13:51 +0000
with message-id <e1qtlol-00bwvs...@fasolo.debian.org>
and subject line Bug#1037855: fixed in seqan-needle 1.0.1.0.1.git.439eeab+ds-1
has caused the Debian Bug report #1037855,
regarding seqan-needle: 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.)
--
1037855: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037855
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:seqan-needle
Version: 1.0.1.0.0.git.3011926+ds-4
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/seqan-needle_1.0.1.0.0.git.3011926+ds-4_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
[...]
int main() {}
Performing C++ SOURCE FILE Test CONCEPTS_FLAG_BUILTIN failed with the following
output:
Change Dir:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_ed4a1/fast && gmake[2]:
Entering directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82'
/usr/bin/gmake -f CMakeFiles/cmTC_ed4a1.dir/build.make
CMakeFiles/cmTC_ed4a1.dir/build
gmake[3]: Entering directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82'
Building CXX object CMakeFiles/cmTC_ed4a1.dir/src.cxx.o
/usr/bin/c++ -DCONCEPTS_FLAG_BUILTIN
-I/usr/include/seqan3/submodules/sdsl-lite/include -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o
CMakeFiles/cmTC_ed4a1.dir/src.cxx.o -c
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82/src.cxx
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82/src.cxx:1:16:
error: ‘__cpp_concepts’ was not declared in this scope
1 | static_assert (__cpp_concepts >= 201507); int
main() {}
| ^~~~~~~~~~~~~~
gmake[3]: *** [CMakeFiles/cmTC_ed4a1.dir/build.make:78:
CMakeFiles/cmTC_ed4a1.dir/src.cxx.o] Error 1
gmake[3]: Leaving directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82'
gmake[2]: *** [Makefile:127: cmTC_ed4a1/fast] Error 2
gmake[2]: Leaving directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-Gc8K82'
Source file was:
static_assert (__cpp_concepts >= 201507); int main() {}
Determining if the include file sdsl/version.hpp exists failed with the
following output:
Change Dir:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_e0d12/fast && gmake[2]:
Entering directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT'
/usr/bin/gmake -f CMakeFiles/cmTC_e0d12.dir/build.make
CMakeFiles/cmTC_e0d12.dir/build
gmake[3]: Entering directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT'
Building CXX object CMakeFiles/cmTC_e0d12.dir/CheckIncludeFile.cxx.o
/usr/bin/c++ -I/usr/include/seqan3/submodules/sdsl-lite/include -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o
CMakeFiles/cmTC_e0d12.dir/CheckIncludeFile.cxx.o -c
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT/CheckIncludeFile.cxx
In file included from
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT/CheckIncludeFile.cxx:1:
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:27:11: error:
‘uint8_t’ does not name a type
27 | constexpr uint8_t sdsl_version_major = SDSL_VERSION_MAJOR;
| ^~~~~~~
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:12:1: note:
‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include
<cstdint>’?
11 | #include <string>
+++ |+#include <cstdint>
12 |
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:29:11: error:
‘uint8_t’ does not name a type
29 | constexpr uint8_t sdsl_version_minor = SDSL_VERSION_MINOR;
| ^~~~~~~
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:29:11: note:
‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include
<cstdint>’?
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:31:11: error:
‘uint8_t’ does not name a type
31 | constexpr uint8_t sdsl_version_patch = SDSL_VERSION_PATCH;
| ^~~~~~~
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:31:11: note:
‘uint8_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include
<cstdint>’?
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:34:49: error:
‘sdsl_version_major’ was not declared in this scope; did you mean
‘sdsl_version’?
34 | std::string const sdsl_version = std::to_string(sdsl_version_major) +
"." + std::to_string(sdsl_version_minor) + "." +
| ^~~~~~~~~~~~~~~~~~
| sdsl_version
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:34:92: error:
‘sdsl_version_minor’ was not declared in this scope; did you mean
‘sdsl_version’?
34 | std::string const sdsl_version = std::to_string(sdsl_version_major) +
"." + std::to_string(sdsl_version_minor) + "." +
|
^~~~~~~~~~~~~~~~~~
|
sdsl_version
/usr/include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp:35:49: error:
‘sdsl_version_patch’ was not declared in this scope; did you mean
‘sdsl_version’?
35 | std::to_string(sdsl_version_patch);
| ^~~~~~~~~~~~~~~~~~
| sdsl_version
gmake[3]: *** [CMakeFiles/cmTC_e0d12.dir/build.make:78:
CMakeFiles/cmTC_e0d12.dir/CheckIncludeFile.cxx.o] Error 1
gmake[3]: Leaving directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT'
gmake[2]: *** [Makefile:127: cmTC_e0d12/fast] Error 2
gmake[2]: Leaving directory
'/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/CMakeScratch/TryCompile-psxKzT'
dh_auto_configure: error: cd obj-x86_64-linux-gnu && cmake
-DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None
-DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu
-DSEQAN3_NO_LEMON=OFF .. returned exit code 1
make[1]: *** [debian/rules:14: override_dh_auto_configure] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: seqan-needle
Source-Version: 1.0.1.0.1.git.439eeab+ds-1
Done: Michael R. Crusoe <cru...@debian.org>
We believe that the bug you reported is fixed in the latest version of
seqan-needle, 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.
Michael R. Crusoe <cru...@debian.org> (supplier of updated seqan-needle 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: Wed, 09 Aug 2023 17:41:39 +0200
Source: seqan-needle
Architecture: source
Version: 1.0.1.0.1.git.439eeab+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <cru...@debian.org>
Closes: 1037855
Changes:
seqan-needle (1.0.1.0.1.git.439eeab+ds-1) unstable; urgency=medium
.
* New upstream snapshot with gcc-12 compatibility Closes: #1037855
* d/patches: refresh; drop spelling patch (applied upstream).
* d/patches: cherry-pick from upstream for Seqan 3.3.0
* Standards-Version: 4.6.2 (routine-update)
* Set upstream metadata fields: Bug-Submit.
Checksums-Sha1:
7a02fbddf92404ebb536e47cbb9d64b6d8f1cf5e 2256
seqan-needle_1.0.1.0.1.git.439eeab+ds-1.dsc
32b67cc6ebc72cb7299bf49cb6ada5fc1adbdf21 5078184
seqan-needle_1.0.1.0.1.git.439eeab+ds.orig.tar.xz
658f322c1491581e761840ed08df458051a545e8 6008
seqan-needle_1.0.1.0.1.git.439eeab+ds-1.debian.tar.xz
d3d25664e64888051620d3f74877cac4ea8f6523 8564
seqan-needle_1.0.1.0.1.git.439eeab+ds-1_source.buildinfo
Checksums-Sha256:
8cc2e68f30f83e469c7aa97a80709cf4fb6875e9f2776931975651966679dde7 2256
seqan-needle_1.0.1.0.1.git.439eeab+ds-1.dsc
f6233c9f0f1bad059bc3d89ae10ab1936061761c368e91d3ea560fef7c6089da 5078184
seqan-needle_1.0.1.0.1.git.439eeab+ds.orig.tar.xz
83df1f7c5bd089ed29da0d118cd288c4885d3a30b0eb6eeed9a39382ac71c219 6008
seqan-needle_1.0.1.0.1.git.439eeab+ds-1.debian.tar.xz
5e55d97100ac19b8c13e0c7bcd411f2183d7b1f24e2accc8f21d624f30dccf89 8564
seqan-needle_1.0.1.0.1.git.439eeab+ds-1_source.buildinfo
Files:
5e3e3dda10355ca63a224b752b581a30 2256 science optional
seqan-needle_1.0.1.0.1.git.439eeab+ds-1.dsc
c69ac0581513651cd254d5f3013044ca 5078184 science optional
seqan-needle_1.0.1.0.1.git.439eeab+ds.orig.tar.xz
5358f42697c78a4727f9054d8fc92642 6008 science optional
seqan-needle_1.0.1.0.1.git.439eeab+ds-1.debian.tar.xz
87637be2c5f05444ae1a8f2630d1894e 8564 science optional
seqan-needle_1.0.1.0.1.git.439eeab+ds-1_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=M3py
-----END PGP SIGNATURE-----
--- End Message ---
