Your message dated Tue, 12 Jul 2022 21:34:38 +0000
with message-id <[email protected]>
and subject line Bug#1012952: fixed in ivar 1.3.1+dfsg-5
has caused the Debian Bug report #1012952,
regarding ivar: 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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1012952: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012952
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:ivar
Version: 1.3.1+dfsg-4
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/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
--- End Message ---
--- Begin Message ---
Source: ivar
Source-Version: 1.3.1+dfsg-5
Done: Étienne Mollier <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
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
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
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.
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--- End Message ---
