Your message dated Mon, 16 Aug 2021 01:25:48 +0530
with message-id
<CAJN1928jFuJgPKQVWT1mjPCErY-eUFUDJ5C3HyAzHSpNgyM=r...@mail.gmail.com>
and subject line Fix
has caused the Debian Bug report #984250,
regarding murasaki: ftbfs with GCC-11
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.
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--
984250: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984250
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:murasaki
Version: 1.68.6-11
Severity: normal
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/murasaki_1.68.6-11_unstable_gcc11.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
| ^~~~
sequence.cc:1114:97: warning: ‘void* memcpy(void*, const void*, size_t)’
writing to an object of type ‘ShmVector<std::pair<long int, long int>
>::val_type’ {aka ‘struct std::pair<long int, long int>’} with no trivial
copy-assignment; use copy-assignment or copy-initialization instead
[-Wclass-memaccess]
1114 |
memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]);
|
^
In file included from /usr/include/c++/11/bits/stl_algobase.h:64,
from /usr/include/c++/11/bits/stl_tree.h:63,
from /usr/include/c++/11/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘ShmVector<std::pair<long
int, long int> >::val_type’ {aka ‘struct std::pair<long int, long int>’}
declared here
211 | struct pair
| ^~~~
sequence.cc: In destructor ‘BitSequence::~BitSequence()’:
sequence.cc:1394:9: warning: ‘throw’ will always call ‘terminate’ [-Wterminate]
1394 | throw MurasakiException("Couldn't detach System V shared memory
region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno));
|
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence.cc:1394:9: note: in C++11 destructors default to ‘noexcept’
sequence.cc: In member function ‘std::pair<double, long int>
IntervalSet::entropy() const’:
sequence.cc:3332:10: warning: variable ‘shortest’ set but not used
[-Wunused-but-set-variable]
3332 | SeqPos shortest=0,shortlen=length(spaces[0]);
| ^~~~~~~~
In file included from sequence.h:44,
from murasaki.h:24,
from sequence.cc:28:
shmvector.hh: In instantiation of ‘void ShmVector<T>::shmRealloc(size_t) [with
T = std::pair<long int, long int>; size_t = long unsigned int]’:
shmvector.hh:282:5: required from ‘void ShmVector<T>::resize(size_t) [with T
= std::pair<long int, long int>; size_t = long unsigned int]’
sequence.cc:1110:39: required from here
shmvector.hh:225:13: warning: ‘void* memcpy(void*, const void*, size_t)’
writing to an object of type ‘struct std::pair<long int, long int>’ with no
trivial copy-assignment; use copy-assignment or copy-initialization instead
[-Wclass-memaccess]
225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ?
oldByteCapacity:_byteCapacity));
|
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:64,
from /usr/include/c++/11/bits/stl_tree.h:63,
from /usr/include/c++/11/set:60,
from cmultiset.h:33,
from sequence.h:30,
from murasaki.h:24,
from sequence.cc:28:
/usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair<long int,
long int>’ declared here
211 | struct pair
| ^~~~
murasaki.cc: In function ‘void procLocs(LocList&,
std::__cxx11::list<Location>&, int, int)’:
murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used
[-Wunused-but-set-variable]
1008 | bool revZero=false;
| ^~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams
-Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams
-Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams
-Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams
-Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams
-Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc
murasaki_mpi.cc: In function ‘void mpi_hasher_client_mode(BitSequence*)’:
murasaki_mpi.cc:561:9: warning: variable ‘send_done’ set but not used
[-Wunused-but-set-variable]
561 | int send_done;
| ^~~~~~~~~
murasaki_mpi.cc: In function ‘word
mpi_extract_checkSentQueue(std::vector<std::__cxx11::list<AnchorBlock*> >&,
std::vector<std::_Rb_tree_iterator<std::pair<const int, int> > >&,
std::multimap<int, int>&)’:
murasaki_mpi.cc:1025:7: error: use of an operand of type ‘bool’ in ‘operator++’
is forbidden in C++17
1025 | packetsLeft++;
| ^~~~~~~~~~~
mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams
-Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc
make[3]: *** [Makefile:189: murasaki_mpi.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:8: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true"
USE_MPI=YES returned exit code 2
make[1]: *** [debian/rules:22: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:19: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Fix with right tags
--- End Message ---
