[Debian-med-packaging] Bug#1037779: mmseqs2: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:28:39 BST 2023
Package: src:mmseqs2
Version: 14-7e284+ds-1
Severity: normal
Tags: sid trixie
User: debian-gcc at 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
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