Your message dated Thu, 20 Jul 2023 14:40:42 +0000
with message-id <e1qmupe-00d5wo...@fasolo.debian.org>
and subject line Bug#1037700: fixed in ivar 1.4.2+dfsg-1
has caused the Debian Bug report #1037700,
regarding ivar: ftbfs with GCC-13
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 ow...@bugs.debian.org
immediately.)
--
1037700: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037700
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:ivar
Version: 1.3.1+dfsg-7
Severity: normal
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie 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-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/ivar_1.3.1+dfsg-7_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html
[...]
primer_bed.cpp:283:115: error: ‘class primer’ has no member named ‘get_start’;
did you mean ‘set_start’?
283 | auto minmax_start = std::minmax_element(primers.begin(),
primers.end(), [] (primer lhs, primer rhs) {return lhs.get_start() <
rhs.get_start();});
|
^~~~~~~~~
|
set_start
primer_bed.cpp:283:133: error: ‘class primer’ has no member named ‘get_start’;
did you mean ‘set_start’?
283 | auto minmax_start = std::minmax_element(primers.begin(),
primers.end(), [] (primer lhs, primer rhs) {return lhs.get_start() <
rhs.get_start();});
|
^~~~~~~~~
|
set_start
primer_bed.cpp: In lambda function:
primer_bed.cpp:288:115: error: ‘class primer’ has no member named ‘get_end’;
did you mean ‘set_end’?
288 | auto minmax_start = std::minmax_element(primers.begin(),
primers.end(), [] (primer lhs, primer rhs) {return lhs.get_end() <
rhs.get_end();});
|
^~~~~~~
|
set_end
primer_bed.cpp:288:131: error: ‘class primer’ has no member named ‘get_end’;
did you mean ‘set_end’?
288 | auto minmax_start = std::minmax_element(primers.begin(),
primers.end(), [] (primer lhs, primer rhs) {return lhs.get_end() <
rhs.get_end();});
|
^~~~~~~
|
set_end
make[3]: *** [Makefile:398: remove_reads_from_amplicon.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [Makefile:398: primer_bed.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' 'alignment.o'
'-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccIpCNHF.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/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' 'alignment.o'
'-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'alignment.'
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' 'ivar.o' '-shared-libgcc'
'-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccAKmKbn.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/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' 'ivar.o' '-shared-libgcc'
'-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
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/ccSaN496.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.40
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/ccnPgGJ4.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/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' 'trim_primer_quality.o'
'-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccsysYgc.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/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.'
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/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.'
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_consensus_pileup.o'
'-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/ccLUcmne.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/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_consensus_pileup.o'
'-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir'
'call_consensus_pileup.'
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: 1.4.2+dfsg-1
Done: Étienne Mollier <emoll...@debian.org>
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 1037...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 20 Jul 2023 15:22:43 +0200
Source: ivar
Architecture: source
Version: 1.4.2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1037700
Changes:
ivar (1.4.2+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Standards-Version: 4.6.2 (routine-update)
* Fix-warning.patch: refresh.
* forward-build-options.patch: refresh.
* privacy-breach.patch: refresh.
* gcc-11.patch: remove: upstream diverged.
* gcc-11_2.patch: remove: now unneeded.
* gcc-12.patch: remove: applied upstream.
* gcc-13.patch: add: fix ftbfs with gcc-13. (Closes: #1037700)
* d/rules: remove executable bit from test data file.
* d/t/ref/*: refresh reference outputs for autopkgtests.
Checksums-Sha1:
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8424d860241b5fdb7cfbb71d8d8d85d6d9162962 672788 ivar_1.4.2+dfsg.orig.tar.xz
3a75d1842f0737c92dfdf58dc8aaf23c4a9ae94c 45848 ivar_1.4.2+dfsg-1.debian.tar.xz
Checksums-Sha256:
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ivar_1.4.2+dfsg-1.dsc
87fbc667080e95823734eeca0dfcec058ff18f1aca7aff89de7a82217a7d2968 672788
ivar_1.4.2+dfsg.orig.tar.xz
0602b05b42569c97abc2ea96dc117186386d7526dbadf3a4420eaff75a822c15 45848
ivar_1.4.2+dfsg-1.debian.tar.xz
Files:
cceed73710393f64c1ba76061b1f3f08 2205 science optional ivar_1.4.2+dfsg-1.dsc
d2c0875cd8d094e11207d0d185099282 672788 science optional
ivar_1.4.2+dfsg.orig.tar.xz
eb6f1131f2c909659bb4c8d0a5e5c30f 45848 science optional
ivar_1.4.2+dfsg-1.debian.tar.xz
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--- End Message ---
