[Debian-med-packaging] Bug#1012893: anfo: ftbfs with GCC-12

[Matthias Klose]

Package: src:anfo
Version: 0.98-9
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/anfo_0.98-9_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.

[...]
  422 |                 ChunkedReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const std::string& name ) ;
      |                                     ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:747:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  747 |                 std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
      |                      ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:762:35: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  762 |                 FastqReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, bool solexa_scores, char origin ) :
      |                                   ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:772:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  772 |                 std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
      |                      ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:795:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  795 |                 SamReader( std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& n, const string& g ) :
      |                                 ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:806:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  806 |                 std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
      |                      ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:821:28: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  821 |                 SffReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name ) :
      |                            ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:832:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  832 |                 std::auto_ptr< google::protobuf::io::ZeroCopyInputStream > is_ ;
      |                      ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:846:28: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  846 |                 BamReader( auto_ptr< google::protobuf::io::ZeroCopyInputStream > is, const string& name, const string& genome ) ;
      |                            ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
stream.h:880:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  880 |                 std::auto_ptr< google::protobuf::io::ZeroCopyOutputStream > os_ ;
      |                      ^~~~~~~~
/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.cc -o sequence.o >/dev/null 2>&1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:440: all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:466: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:374: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2