[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/ivar_1.3.1+dfsg-4_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.

[...]
Compiler executable checksum: f7019d9afd9ded4088378f1b565ba3a5
call_consensus_pileup.cpp: In function ‘int call_consensus_from_plup(std::istream&, std::string, std::string, uint8_t, double, uint8_t, char, bool)’:
call_consensus_pileup.cpp:138:3: error: ‘strcpy’ was not declared in this scope
  138 |   strcpy(o, out_file.c_str());
      |   ^~~~~~
call_consensus_pileup.cpp:2:1: note: ‘strcpy’ is defined in header ‘<cstring>’; did you forget to ‘#include <cstring>’?
    1 | #include "call_consensus_pileup.h"
  +++ |+#include <cstring>
    2 |
make[3]: *** [Makefile:398: call_consensus_pileup.o] Error 1
make[3]: *** Waiting for unfinished jobs....
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/ccwaNn59.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.38
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'remove_reads_from_amplicon.'
ivar.cpp: In function ‘int main(int, char**)’:
ivar.cpp:487:14: error: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Werror=mismatched-new-delete]
  487 |       delete files;
      |              ^~~~~
ivar.cpp:467:33: note: returned from ‘void* operator new [](std::size_t)’
  467 |     char **files = new char*[100];
      |                                 ^
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/ccyGq2cC.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.38
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/ccA2J4m4.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.38
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o allele_functions.o /tmp/cc8soYfG.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.38
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccQj6aXz.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.38
cc1plus: all warnings being treated as errors
make[3]: *** [Makefile:398: ivar.o] Error 1
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/ccYrbZBf.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.38
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'allele_functions.'
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.'
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/12/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/12/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'primer_bed.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:371: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:312: 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

Hello,

Bug #1012952 in ivar reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/ivar/-/commit/c86f598906367fabeb65f1832d5396d033e6b7d9
Closes: #1012952
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1012952

We believe that the bug you reported is fixed in the latest version of
ivar, 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 1012952@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emollier@debian.org> (supplier of updated ivar 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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Tue, 12 Jul 2022 23:11:44 +0200
Source: ivar
Architecture: source
Version: 1.3.1+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Closes: 1012952
Changes:
 ivar (1.3.1+dfsg-5) unstable; urgency=medium
 .
   * Add gcc-12.patch: fix ftbfs with gcc-12. (Closes: #1012952)
   * Standards-Version: 4.6.1 (routine-update)
   * d/s/lintian-overrides: update to new lintian semantics.
Checksums-Sha1:
 dc836ac305dd52d6eda67b523720659e7067a373 2205 ivar_1.3.1+dfsg-5.dsc
 849ed9c499b2a889ed817a01529645eb2d7395e6 45860 ivar_1.3.1+dfsg-5.debian.tar.xz
Checksums-Sha256:
 cad449841d1333dc5b8fff0dab06291b203c06ef8b6c1c76a4f65b0b837c24d6 2205 ivar_1.3.1+dfsg-5.dsc
 2ed2fb6a470874428a478be6c817cce3fecb2a78665e3b577037398407272a96 45860 ivar_1.3.1+dfsg-5.debian.tar.xz
Files:
 38a029d98312a3757a2a06cd76837de4 2205 science optional ivar_1.3.1+dfsg-5.dsc
 fe12894943b7c6f4f245eb6b39489b9f 45860 science optional ivar_1.3.1+dfsg-5.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
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=NgwV
-----END PGP SIGNATURE-----