[Debian-med-packaging] Bug#1042148: metaeuk: FTBFS: Util.h:87:12: error: ‘uint64_t’ does not name a type
Lucas Nussbaum
lucas at debian.org
Wed Jul 26 20:52:42 BST 2023
Source: metaeuk
Version: 6-a5d39d9+ds-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lucas@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.
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