Your message dated Thu, 16 Sep 2021 20:48:30 +0000
with message-id <[email protected]>
and subject line Bug#984067: fixed in ivar 1.3.1+dfsg-2
has caused the Debian Bug report #984067,
regarding ivar: ftbfs with GCC-11
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
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--
984067: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984067
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:ivar
Version: 1.3+dfsg-1
Severity: normal
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/ivar_1.3+dfsg-1_unstable_gcc11.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.
[...]
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-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.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g
-std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
Using built-in specs.
COLLECT_GCC=g++
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 11-20210227-1'
--with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs
--enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr
--with-gcc-major-version-only --program-suffix=-11
--program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id
--libexecdir=/usr/lib --without-included-gettext --enable-threads=posix
--libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu
--enable-libstdcxx-debug --enable-libstdcxx-time=yes
--with-default-libstdcxx-abi=new --enable-gnu-unique-object
--disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib
--enable-libphobos-checking=release --with-target-system-zlib=auto
--enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet
--with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32
--enable-multilib --with-tune=generic
--enable-offload-targets=nvptx-none=/packages/gcc/11/gcc-11-11-20210227/debian/t
mp-nvptx/usr,amdgcn-amdhsa=/packages/gcc/11/gcc-11-11-20210227/debian/tmp-gcn/usr
--without-cuda-driver --enable-checking=yes,extra,rtl --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
--with-build-config=bootstrap-lto-lean --enable-link-serialization=32
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.0.1 20210227 (experimental) [master revision
ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d] (Debian
11-20210227-1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c'
'-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/lib/gcc/x86_64-linux-gnu/11/cc1plus -quiet -v -I . -I .. -imultiarch
x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2
call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp
-mtune=generic -march=x86-64 -g -Wdate-time -Wall -Wextra -Werror -std=c++11
-version -fasynchronous-unwind-tables -o /tmp/ccHC7IGP.s
GNU C++11 (Debian 11-20210227-1) version 11.0.1 20210227 (experimental) [master
revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d]
(x86_64-linux-gnu)
compiled by GNU C version 11.0.1 20210227 (experimental) [master
revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d], GMP
version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/11"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/include-fixed"
ignoring nonexistent directory
"/usr/lib/gcc/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/x86_64-linux-gnu/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/x86_64-linux-gnu/11/include
/usr/local/include
/usr/include/x86_64-linux-gnu
/usr/include
End of search list.
GNU C++11 (Debian 11-20210227-1) version 11.0.1 20210227 (experimental) [master
revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d]
(x86_64-linux-gnu)
compiled by GNU C version 11.0.1 20210227 (experimental) [master
revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d], GMP
version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
Compiler executable checksum: 2900c290e29b54415706f52c8eebe364
cc1plus: all warnings being treated as errors
make[3]: *** [Makefile:389: ivar.o] Error 1
make[3]: *** Waiting for unfinished jobs....
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-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/ccjBTk0p.s
GNU assembler version 2.35.2 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-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' '-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/cc1GXrdE.s
GNU assembler version 2.35.2 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-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.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-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/ccHC7IGP.s
GNU assembler version 2.35.2 (x86_64-linux-gnu) using BFD version (GNU Binutils
for Debian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D'
'_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c'
'-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
'-dumpdir' 'call_variants.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:362: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:303: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 returned exit code 2
make: *** [debian/rules:9: 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-2
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: Thu, 16 Sep 2021 22:22:30 +0200
Source: ivar
Architecture: source
Version: 1.3.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 984067
Changes:
ivar (1.3.1+dfsg-2) unstable; urgency=medium
.
* add forward-build-options.patch; build ivar with hardened build options
* add gcc-11.patch; fixes ftbfs with Gcc 11 (Closes: #984067)
* d/salsa-ci.yml: allow reproducible build test to fail, for the moment
* update d/s/lintian-overrides to match the new lintian semantics against the
false positive
* add privacy-breach.patch to point to the local diagram in cookbook.html,
instead of the github page
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--- End Message ---
