Your message dated Fri, 24 Jun 2022 20:41:38 +0000
with message-id <[email protected]>
and subject line Bug#1013000: fixed in mira 4.9.6-7
has caused the Debian Bug report #1013000,
regarding mira: ftbfs with GCC-12
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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--
1013000: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1013000
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:mira
Version: 4.9.6-6
Severity: normal
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-gcc-12
[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/mira_4.9.6-6_unstable_gcc12.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.
[...]
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of
declaring the Bind placeholders (_1, _2, ...) in the global namespace is
deprecated. Please use <boost/bind/bind.hpp> + using namespace
boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the
current behavior.’
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\"
-DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\"
-DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1
-DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1
-DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1
-DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1
-DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1
-DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/
-DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/
-DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1
-DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src
-Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2
-ffile-prefix-map=
/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security
-I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include
-Werror=uninitialized -Werror=return-type -Werror=parentheses
-Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o
assembly_pbcorrect.C
In file included from
/usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
from
/usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
from /usr/include/boost/shared_ptr.hpp:17,
from /usr/include/boost/regex/v4/regex_workaround.hpp:44,
from /usr/include/boost/regex/v4/regex.hpp:32,
from /usr/include/boost/regex.hpp:31,
from assembly_misc.C:31:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of
declaring the Bind placeholders (_1, _2, ...) in the global namespace is
deprecated. Please use <boost/bind/bind.hpp> + using namespace
boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the
current behavior.’
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
assembly_pbcorrect.C:59: warning: "CEBUG" redefined
59 | #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}}
|
assembly_pbcorrect.C:45: note: this is the location of the previous definition
45 | #define CEBUG(bla)
|
assembly_misc.C: In member function ‘void Assembly::priv_phahelper(const
std::string&, const std::string&, uint32, bool, int32, std::string,
std::string, std::string)’:
assembly_misc.C:376:17: warning: use of an operand of type ‘bool’ in
‘operator++’ is deprecated [-Wdeprecated]
376 | countedthisseq++;
| ^~~~~~~~~~~~~~
assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const
std::string&, const std::string&, uint32, bool, int32, std::string,
std::string, std::string) [with TVHASH_T = long unsigned int; std::string =
std::__cxx11::basic_string<char>; uint32 = unsigned int; int32 = int]’:
assembly_misc.C:471:30: required from here
assembly_misc.C:376:17: warning: use of an operand of type ‘bool’ in
‘operator++’ is deprecated [-Wdeprecated]
assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const
std::string&, const std::string&, uint32, bool, int32, std::string,
std::string, std::string) [with TVHASH_T = VLuint<128>; std::string =
std::__cxx11::basic_string<char>; uint32 = unsigned int; int32 = int]’:
assembly_misc.C:473:31: required from here
assembly_misc.C:376:17: warning: use of an operand of type ‘bool’ in
‘operator++’ is deprecated [-Wdeprecated]
assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const
std::string&, const std::string&, uint32, bool, int32, std::string,
std::string, std::string) [with TVHASH_T = VLuint<256>; std::string =
std::__cxx11::basic_string<char>; uint32 = unsigned int; int32 = int]’:
assembly_misc.C:475:31: required from here
assembly_misc.C:376:17: warning: use of an operand of type ‘bool’ in
‘operator++’ is deprecated [-Wdeprecated]
assembly_misc.C: In instantiation of ‘void Assembly::priv_phahelper(const
std::string&, const std::string&, uint32, bool, int32, std::string,
std::string, std::string) [with TVHASH_T = VLuint<512>; std::string =
std::__cxx11::basic_string<char>; uint32 = unsigned int; int32 = int]’:
assembly_misc.C:477:31: required from here
assembly_misc.C:376:17: warning: use of an operand of type ‘bool’ in
‘operator++’ is deprecated [-Wdeprecated]
In file included from /usr/include/boost/bind.hpp:30,
from ../../src/mira/stringcontainer.H:38,
from ../../src/mira/multitag.H:40,
from ../../src/mira/read.H:38,
from ../../src/mira/readpool.H:41,
from ../../src/mira/pcrcontainer.H:30,
from ../../src/mira/contig.H:42,
from ../../src/mira/assembly_info.H:33,
from ../../src/mira/assembly.H:33,
from assembly_pbcorrect.C:26:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of
declaring the Bind placeholders (_1, _2, ...) in the global namespace is
deprecated. Please use <boost/bind/bind.hpp> + using namespace
boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the
current behavior.’
36 | BOOST_PRAGMA_MESSAGE(
| ^~~~~~~~~~~~~~~~~~~~
cc1plus: some warnings being treated as errors
make[6]: *** [Makefile:637: hashstats_sdbg.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/mira'
make[5]: *** [Makefile:524: all] Error 2
make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/mira'
make[4]: *** [Makefile:399: all-recursive] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:416: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:363: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make[1]: *** [debian/rules:39: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: mira
Source-Version: 4.9.6-7
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
mira, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated mira 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 24 Jun 2022 20:01:35 +0000
Source: mira
Architecture: source
Version: 4.9.6-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 1013000
Changes:
mira (4.9.6-7) unstable; urgency=medium
.
* Team Upload.
* Add patch to fix gcc-12 FTBFS (Closes: #1013000)
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