[Debian-med-packaging] Bug#1012952: ivar: ftbfs with GCC-12

Thu Jun 16 13:09:49 BST 2022

Package: src:ivar
Version: 1.3.1+dfsg-4
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/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