Your message dated Thu, 27 Jul 2023 12:08:23 +0000
with message-id <e1qozn5-009wgh...@fasolo.debian.org>
and subject line Bug#1042148: fixed in metaeuk 6-a5d39d9+ds-3
has caused the Debian Bug report #1042148,
regarding metaeuk: FTBFS: Util.h:87:12: error: ‘uint64_t’ does not name a type
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.)
--
1042148: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042148
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: metaeuk
Version: 6-a5d39d9+ds-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20230726 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/mmseqs/src && /usr/bin/c++
> -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1
> -DOPENMP=1 -I/<<PKGBUILDDIR>>/lib/mmseqs/lib/tinyexpr
> -I/<<PKGBUILDDIR>>/lib/mmseqs/lib/microtar -I/<<PKGBUILDDIR>>/lib/mmseqs/lib
> -I/<<PKGBUILDDIR>>/lib/mmseqs/lib/simd -I/<<PKGBUILDDIR>>/lib/mmseqs/lib/alp
> -I/<<PKGBUILDDIR>>/lib/mmseqs/lib/cacode
> -I/<<PKGBUILDDIR>>/lib/mmseqs/lib/ksw2
> -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/generated
> -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/mmseqs/generated
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/alignment
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/clustering
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/commons
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/multihit
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/prefiltering
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/linclust
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/taxonomy
> -I/<<PKGBUILDDIR>>/lib/mmseqs/src/util -I/<<PKGBUILDDIR>>/lib/mmseqs/src/. -g
> -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fsigned-char
> -std=c++1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions
> -fopenmp -MD -MT
> lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -MF
> CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o.d -o
> CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -c
> /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/Matcher.cpp
> In file included from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/MultiParam.h:15,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:15,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Sequence.h:10,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/DBReader.h:13,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/IndexReader.h:4,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/Alignment.h:4,
> from
> /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/Alignment.cpp:1:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:87:12: error: ‘uint64_t’ does
> not name a type
> 87 | static uint64_t getL2CacheSize();
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:11:1: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> 10 | #include "MMseqsMPI.h"
> +++ |+#include <cstdint>
> 11 |
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: error: ‘uint64_t’ does
> not name a type
> 360 | static uint64_t revComplement(const uint64_t kmer, const int k);
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> In file included from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/MultiParam.h:15,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:15,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Sequence.h:10,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/DBReader.h:13,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/IndexReader.h:4,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/Alignment.h:4,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/Main.cpp:1:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:87:12: error: ‘uint64_t’ does
> not name a type
> 87 | static uint64_t getL2CacheSize();
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:11:1: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> 10 | #include "MMseqsMPI.h"
> +++ |+#include <cstdint>
> 11 |
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: error: ‘uint64_t’ does
> not name a type
> 360 | static uint64_t revComplement(const uint64_t kmer, const int k);
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> In file included from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:5,
> from
> /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/MsaFilter.cpp:5:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:87:12: error: ‘uint64_t’ does
> not name a type
> 87 | static uint64_t getL2CacheSize();
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:11:1: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> 10 | #include "MMseqsMPI.h"
> +++ |+#include <cstdint>
> 11 |
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: error: ‘uint64_t’ does
> not name a type
> 360 | static uint64_t revComplement(const uint64_t kmer, const int k);
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1131:18: error:
> ‘uint32_t’ does not name a type
> 1131 | static const uint32_t DBTYPE_MASK = 0x0000FFFF;
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/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>>/lib/mmseqs/src/commons/Parameters.h:1131:18: error:
> ‘uint32_t’ does not name a type
> 1131 | static const uint32_t DBTYPE_MASK = 0x0000FFFF;
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/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>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static bool Parameters::isEqualDbtype(int, int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1134:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1134 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static const char* Parameters::getDbTypeName(int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1138:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1138 | switch (dbtype & DBTYPE_MASK) {
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static bool Parameters::isEqualDbtype(int, int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1134:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1134 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static const char* Parameters::getDbTypeName(int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1138:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1138 | switch (dbtype & DBTYPE_MASK) {
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> In file included from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/MultiParam.h:15,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:15,
> from
> /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:26:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:87:12: error: ‘uint64_t’ does
> not name a type
> 87 | static uint64_t getL2CacheSize();
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:11:1: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> 10 | #include "MMseqsMPI.h"
> +++ |+#include <cstdint>
> 11 |
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: error: ‘uint64_t’ does
> not name a type
> 360 | static uint64_t revComplement(const uint64_t kmer, const int k);
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Util.h:360:12: note: ‘uint64_t’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h: In constructor
> ‘Debug::Progress::Progress()’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:169:69: error: ‘SIZE_MAX’ was
> not declared in this scope
> 169 | Progress() : currentPos(0), prevPrintedId(0),
> totalEntries(SIZE_MAX){
> |
> ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:12:1: note: ‘SIZE_MAX’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> 11 | #include <sys/stat.h>
> +++ |+#include <cstdint>
> 12 |
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h: In member function ‘void
> Debug::Progress::updateProgress()’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:184:34: error: ‘SIZE_MAX’ was
> not declared in this scope
> 184 | if(totalEntries==SIZE_MAX) {
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:184:34: note: ‘SIZE_MAX’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:218:34: error: ‘SIZE_MAX’ was
> not declared in this scope
> 218 | if(totalEntries==SIZE_MAX){
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Debug.h:218:34: note: ‘SIZE_MAX’ is
> defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
> In file included from /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Sequence.h:10,
> from
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/ProfileStates.h:11,
> from
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/SubstitutionMatrix.h:13,
> from /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/MsaFilter.h:9,
> from
> /<<PKGBUILDDIR>>/lib/mmseqs/src/alignment/MsaFilter.cpp:7:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: At global scope:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1131:18: error:
> ‘uint32_t’ does not name a type
> 1131 | static const uint32_t DBTYPE_MASK = 0x0000FFFF;
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/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>>/lib/mmseqs/src/commons/Parameters.h:1131:18: error:
> ‘uint32_t’ does not name a type
> 1131 | static const uint32_t DBTYPE_MASK = 0x0000FFFF;
> | ^~~~~~~~
> /<<PKGBUILDDIR>>/lib/mmseqs/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>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static bool Parameters::isEqualDbtype(int, int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1134:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1134 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static bool Parameters::isEqualDbtype(int, int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1134:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1134 | return ((type1 & DBTYPE_MASK) == (type2 & DBTYPE_MASK));
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static const char* Parameters::getDbTypeName(int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1138:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1138 | switch (dbtype & DBTYPE_MASK) {
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h: In static member
> function ‘static const char* Parameters::getDbTypeName(int)’:
> /<<PKGBUILDDIR>>/lib/mmseqs/src/commons/Parameters.h:1138:26: error:
> ‘DBTYPE_MASK’ was not declared in this scope; did you mean ‘DBTYPE_MSA_DB’?
> 1138 | switch (dbtype & DBTYPE_MASK) {
> | ^~~~~~~~~~~
> | DBTYPE_MSA_DB
> make[3]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make:135:
> lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o]
> Error 1
The full build log is available from:
http://qa-logs.debian.net/2023/07/26/metaeuk_6-a5d39d9+ds-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230726;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: metaeuk
Source-Version: 6-a5d39d9+ds-3
Done: Sascha Steinbiss <sa...@debian.org>
We believe that the bug you reported is fixed in the latest version of
metaeuk, 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 1042...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sascha Steinbiss <sa...@debian.org> (supplier of updated metaeuk 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: Thu, 27 Jul 2023 12:27:38 +0200
Source: metaeuk
Architecture: source
Version: 6-a5d39d9+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Sascha Steinbiss <sa...@debian.org>
Closes: 1042148
Changes:
metaeuk (6-a5d39d9+ds-3) unstable; urgency=medium
.
[ Andreas Tille ]
* Team upload.
* d/tests/control:
Architecture: amd64 arm64 mips64el ppc64el ia64 kfreebsd-amd64 riscv64
Depends: metaeuk
* Drop redundant debian/gbp.conf
* Add salsa-ci file (routine-update)
.
[ Sascha Steinbiss ]
* Fix FTBFS with GCC 13.
Closes: #1042148
Checksums-Sha1:
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b6fa5549eb06e37ce8fc3dd587c70e1f5cb1aad4 7588
metaeuk_6-a5d39d9+ds-3.debian.tar.xz
0670e0ae0703f7d7828be63ac4444f140dfef43f 8194
metaeuk_6-a5d39d9+ds-3_amd64.buildinfo
Checksums-Sha256:
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Files:
e018f586abdfdf9e64c211299fa53471 2249 science optional
metaeuk_6-a5d39d9+ds-3.dsc
a66a9326522d2017cc14977b08a01e40 7588 science optional
metaeuk_6-a5d39d9+ds-3.debian.tar.xz
f0169d3559a7c64452023cf431a18e16 8194 science optional
metaeuk_6-a5d39d9+ds-3_amd64.buildinfo
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