Your message dated Sun, 30 Jul 2023 12:42:08 +0000
with message-id <e1qq5ko-008p0p...@fasolo.debian.org>
and subject line Bug#1037779: fixed in mmseqs2 14-7e284+ds-2
has caused the Debian Bug report #1037779,
regarding mmseqs2: 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.)
--
1037779: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037779
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:mmseqs2
Version: 14-7e284+ds-1
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/mmseqs2_14-7e284+ds-1_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
[...]
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/commons/Parameters.h:16:1: note: ‘uint32_t’ is defined in
header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
15 | #include "MultiParam.h"
+++ |+#include <cstdint>
16 |
/<<PKGBUILDDIR>>/src/commons/Debug.h:218:34: error: ‘SIZE_MAX’ was not declared
in this scope
218 | if(totalEntries==SIZE_MAX){
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/commons/Debug.h:218:34: note: ‘SIZE_MAX’ is defined in
header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/src/commons/Parameters.h: In static member function ‘static
bool Parameters::isEqualDbtype(int, int)’:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1135:26: error: ‘DBTYPE_MASK’ was not
declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
1135 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
| ^~~~~~~~~~~
| DBTYPE_MSA_DB
/<<PKGBUILDDIR>>/src/commons/Parameters.h: In static member function ‘static
bool Parameters::isEqualDbtype(int, int)’:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1135:26: error: ‘DBTYPE_MASK’ was not
declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
1135 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
| ^~~~~~~~~~~
| DBTYPE_MSA_DB
/<<PKGBUILDDIR>>/src/commons/Parameters.h: In static member function ‘static
const char* Parameters::getDbTypeName(int)’:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1139:26: error: ‘DBTYPE_MASK’ was not
declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
1139 | switch (dbtype & DBTYPE_MASK) {
| ^~~~~~~~~~~
| DBTYPE_MSA_DB
/<<PKGBUILDDIR>>/src/commons/Parameters.h: In static member function ‘static
const char* Parameters::getDbTypeName(int)’:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1139:26: error: ‘DBTYPE_MASK’ was not
declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
1139 | switch (dbtype & DBTYPE_MASK) {
| ^~~~~~~~~~~
| DBTYPE_MSA_DB
In file included from /<<PKGBUILDDIR>>/src/commons/Sequence.h:10,
from /<<PKGBUILDDIR>>/src/commons/ProfileStates.h:11,
from /<<PKGBUILDDIR>>/src/commons/SubstitutionMatrix.h:13,
from /<<PKGBUILDDIR>>/src/alignment/MsaFilter.h:9,
from /<<PKGBUILDDIR>>/src/alignment/MsaFilter.cpp:7:
/<<PKGBUILDDIR>>/src/commons/Parameters.h: At global scope:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1132:18: error: ‘uint32_t’ does not
name a type
1132 | static const uint32_t DBTYPE_MASK = 0x0000FFFF;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/commons/Parameters.h:16:1: note: ‘uint32_t’ is defined in
header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
15 | #include "MultiParam.h"
+++ |+#include <cstdint>
16 |
/<<PKGBUILDDIR>>/src/commons/Parameters.h: In static member function ‘static
bool Parameters::isEqualDbtype(int, int)’:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1135:26: error: ‘DBTYPE_MASK’ was not
declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
1135 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
| ^~~~~~~~~~~
| DBTYPE_MSA_DB
/<<PKGBUILDDIR>>/src/commons/Parameters.h: In static member function ‘static
const char* Parameters::getDbTypeName(int)’:
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1139:26: error: ‘DBTYPE_MASK’ was not
declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
1139 | switch (dbtype & DBTYPE_MASK) {
| ^~~~~~~~~~~
| DBTYPE_MSA_DB
make[4]: *** [src/CMakeFiles/mmseqs-framework.dir/build.make:135:
src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [src/CMakeFiles/mmseqs-framework.dir/build.make:107:
src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o] Error 1
/<<PKGBUILDDIR>>/src/commons/Parameters.h:1160:5: warning: control reaches end
of non-void function [-Wreturn-type]
1160 | }
| ^
make[4]: *** [src/CMakeFiles/mmseqs-framework.dir/build.make:79:
src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o] Error 1
make[4]: *** [src/CMakeFiles/mmseqs-framework.dir/build.make:177:
src/CMakeFiles/mmseqs-framework.dir/alignment/StripedSmithWaterman.cpp.o] Error
1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build_avx2'
make[3]: *** [CMakeFiles/Makefile2:602:
src/CMakeFiles/mmseqs-framework.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build_avx2'
make[2]: *** [Makefile:139: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build_avx2'
dh_auto_build: error: cd build_avx2 && make -j8 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:39: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:20: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: mmseqs2
Source-Version: 14-7e284+ds-2
Done: Bo YU <tsu.y...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
mmseqs2, 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.
Bo YU <tsu.y...@gmail.com> (supplier of updated mmseqs2 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: SHA256
Format: 1.8
Date: Fri, 28 Jul 2023 10:31:23 +0800
Source: mmseqs2
Architecture: source
Version: 14-7e284+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Bo YU <tsu.y...@gmail.com>
Closes: 1037779
Changes:
mmseqs2 (14-7e284+ds-2) unstable; urgency=medium
.
* Team upload.
* Add fix-gcc-13.patch to fix gcc-13 build issue. (Closes: #1037779)
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