[Debian-med-packaging] Bug#957519: mapsembler2: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 12:05:45 BST 2020
Package: src:mapsembler2
Version: 2.2.4+dfsg-3
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10
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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/mapsembler2_2.2.4+dfsg-3_unstable_gcc10.log
The last lines of the build log are at the end of this report.
To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html
[...]
| | |
| | uint64_t {aka long unsigned int}
| long long int
| %li
../minia/Debloom.cpp: In function ‘Set* load_false_positives()’:
../minia/Debloom.cpp:280:112: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘int64_t’ {aka ‘long int’} [-Wformat=]
280 | if ((NbInsertedKmers%10000)==0) fprintf (stderr,(char*)"%cInsert false positive Kmers in hash table %lld",13,NbInsertedKmers);
| ~~~^ ~~~~~~~~~~~~~~~
| | |
| | int64_t {aka long int}
| long long int
| %ld
../minia/Debloom.cpp:284:36: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘int64_t’ {aka ‘long int’} [-Wformat=]
284 | fprintf (stderr,"\nInserted %lld false positive kmers in the hash structure.\n\n",NbInsertedKmers);
| ~~~^ ~~~~~~~~~~~~~~~
| | |
| long long int int64_t {aka long int}
| %ld
../minia/Debloom.cpp: In function ‘void print_size_summary(FPSet*)’:
../minia/Debloom.cpp:445:50: warning: format ‘%lli’ expects argument of type ‘long long int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
445 | fprintf(stderr, "Size of the FP table : %lli FP x %d bits = %.2lf MB \n", fp->capacity(), bits_per_FP_element, toMB((double)(size_T1)) );
| ~~~^ ~~~~~~~~~~~~~~
| | |
| long long int uint64_t {aka long unsigned int}
| %li
../minia/Debloom.cpp:448:47: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
448 | fprintf(stderr," Total %.2lf MB for %lld solid kmers ==> %.2lf bits / solid kmer\n\n", toMB(total_size), nbkmers_solid, total_size / nbkmers_solid);
| ~~~^ ~~~~~~~~~~~~~
| | |
| long long int uint64_t {aka long unsigned int}
| %ld
../minia/Debloom.cpp: In function ‘void print_size_summary(FPSetCascading4*)’:
../minia/Debloom.cpp:465:47: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
465 | fprintf(stderr," Total %.2lf MB for %lld solid kmers ==> %.2lf bits / solid kmer\n\n", toMB(total_size), nbkmers_solid, total_size / nbkmers_solid);
| ~~~^ ~~~~~~~~~~~~~
| | |
| long long int uint64_t {aka long unsigned int}
| %ld
../minia/Debloom.cpp: In function ‘void end_debloom_partition(bool)’:
../minia/Debloom.cpp:29:11: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
29 | ftruncate(fileno(F_debloom_write), 0); //erase previous file
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../minia/OAHash.o -c ../minia/OAHash.cpp -O3 -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/mapsembler2_extend=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial
g++ -o commons.o -c commons.cpp -O3 -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/mapsembler2_extend=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial
g++ -o IterativeExtensions.o -c IterativeExtensions.cpp -O3 -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/mapsembler2_extend=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial
g++ -o Fragment_Bank.o -c Fragment_Bank.cpp -O3 -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/mapsembler2_extend=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial
In file included from Fragment.h:18,
from Fragment_Bank.h:3,
from Fragment_Bank.cpp:7:
GraphOutput.h:51:11: error: redefinition of ‘struct std::hash<__int128 unsigned>’
51 | struct hash<__uint128_t> : public unary_function<__uint128_t, size_t>
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/basic_string.h:6757,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/ostream:38,
from /usr/include/c++/10/iostream:39,
from Fragment_Bank.h:1,
from Fragment_Bank.cpp:7:
/usr/include/c++/10/bits/functional_hash.h:175:3: note: previous definition of ‘struct std::hash<__int128 unsigned>’
175 | _Cxx_hashtable_define_trivial_hash(__GLIBCXX_TYPE_INT_N_0 unsigned)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [makefile:116: Fragment_Bank.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/mapsembler2_extend'
make[1]: *** [debian/rules:28: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:23: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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