[Debian-med-packaging] Bug#984073: kallisto: ftbfs with GCC-11

Matthias Klose doko at debian.org
Wed Mar 3 16:13:47 GMT 2021 

Package: src:kallisto
Version: 0.46.2+dfsg-2
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
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

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