Your message dated Thu, 04 Mar 2021 18:48:26 +0000
with message-id <[email protected]>
and subject line Bug#984073: fixed in kallisto 0.46.2+dfsg-3
has caused the Debian Bug report #984073,
regarding kallisto: 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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
984073: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984073
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:kallisto
Version: 0.46.2+dfsg-2
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/kallisto_0.46.2+dfsg-2_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.
[...]
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build
cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install
--strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
--check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/kallisto_core.dir/build.make
src/CMakeFiles/kallisto_core.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake
--color=
Dependee
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake"
is newer than depender
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto_core.dir/depend.internal".
Dependee
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake"
is newer than depender
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/CMakeFiles/kallisto_core.dir/depend.internal".
Scanning dependencies of target kallisto_core
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/kallisto_core.dir/build.make
src/CMakeFiles/kallisto_core.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o
[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o
[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c
/<<PKGBUILDDIR>>/src/BUSData.cpp
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o
-c /<<PKGBUILDDIR>>/src/Bootstrap.cpp
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o
-c /<<PKGBUILDDIR>>/src/BUSTools.cpp
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o
-c /<<PKGBUILDDIR>>/src/GeneModel.cpp
[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o
-c /<<PKGBUILDDIR>>/src/H5Writer.cpp
[ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c
/<<PKGBUILDDIR>>/src/Kmer.cpp
[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o
-c /<<PKGBUILDDIR>>/src/KmerIndex.cpp
[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o
CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c
/<<PKGBUILDDIR>>/src/KmerIterator.cpp
[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c
/<<PKGBUILDDIR>>/src/Merge.cpp
[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o
CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c
/<<PKGBUILDDIR>>/src/MinCollector.cpp
[ 52%] Building CXX object
src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++
-I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -std=c++11 -o
CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c
/<<PKGBUILDDIR>>/src/PlaintextWriter.cpp
/<<PKGBUILDDIR>>/src/MinCollector.cpp: In member function ‘std::vector<int>
MinCollector::intersectECs(std::vector<std::pair<KmerEntry, int> >&) const’:
/<<PKGBUILDDIR>>/src/MinCollector.cpp:194:21: error: ‘numeric_limits’ is not a
member of ‘std’
194 | int minpos = std::numeric_limits<int>::max();
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/MinCollector.cpp:194:36: error: expected
primary-expression before ‘int’
194 | int minpos = std::numeric_limits<int>::max();
| ^~~
/<<PKGBUILDDIR>>/src/MinCollector.cpp: In member function ‘double
MinCollector::get_mean_frag_len(bool) const’:
/<<PKGBUILDDIR>>/src/MinCollector.cpp:294:19: error: ‘numeric_limits’ is not a
member of ‘std’
294 | return std::numeric_limits<double>::max();
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/MinCollector.cpp:294:34: error: expected
primary-expression before ‘double’
294 | return std::numeric_limits<double>::max();
| ^~~~~~
/<<PKGBUILDDIR>>/src/MinCollector.cpp:294:34: error: expected ‘;’ before
‘double’
294 | return std::numeric_limits<double>::max();
| ^~~~~~
| ;
/<<PKGBUILDDIR>>/src/MinCollector.cpp:294:40: error: expected unqualified-id
before ‘>’ token
294 | return std::numeric_limits<double>::max();
| ^
make[3]: *** [src/CMakeFiles/kallisto_core.dir/build.make:202:
src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:145: src/CMakeFiles/kallisto_core.dir/all]
Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:152: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:14: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: kallisto
Source-Version: 0.46.2+dfsg-3
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kallisto, 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.
Nilesh Patra <[email protected]> (supplier of updated kallisto 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, 04 Mar 2021 23:54:34 +0530
Source: kallisto
Architecture: source
Version: 0.46.2+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 984073
Changes:
kallisto (0.46.2+dfsg-3) unstable; urgency=medium
.
* Team Upload.
* debian/patches/gcc11.patch: Fix gcc-11 FTBFS (Closes: #984073)
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