[Debian-med-packaging] Bug#1013000: mira: ftbfs with GCC-12

[Matthias Klose]

Package: src:mira
Version: 4.9.6-6
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
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