[Debian-med-packaging] Bug#957747: racon: ftbfs with GCC-10

Fri Apr 17 12:09:50 BST 2020

Package: src:racon
Version: 1.4.10-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/racon_1.4.10-1_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
  189 |         throw std::invalid_argument("[bioparser::createParser] error: "
      |                    ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:263:24: error: ‘invalid_argument’ is not a member of ‘std’
  263 |             throw std::invalid_argument("[bioparser::FastaParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool bioparser::FastaParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t, bool)’:
/usr/include/bioparser/bioparser.hpp:287:28: error: ‘invalid_argument’ is not a member of ‘std’
  287 |                 throw std::invalid_argument("[bioparser::FastaParser] error: "
      |                            ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:381:24: error: ‘invalid_argument’ is not a member of ‘std’
  381 |             throw std::invalid_argument("[bioparser::FastqParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool bioparser::FastqParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t, bool)’:
/usr/include/bioparser/bioparser.hpp:407:28: error: ‘invalid_argument’ is not a member of ‘std’
  407 |                 throw std::invalid_argument("[bioparser::FastqParser] error: "
      |                            ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:545:24: error: ‘invalid_argument’ is not a member of ‘std’
  545 |             throw std::invalid_argument("[bioparser::MhapParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool bioparser::MhapParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t, bool)’:
/usr/include/bioparser/bioparser.hpp:567:28: error: ‘invalid_argument’ is not a member of ‘std’
  567 |                 throw std::invalid_argument("[bioparser::MhapParser] error: "
      |                            ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:675:24: error: ‘invalid_argument’ is not a member of ‘std’
  675 |             throw std::invalid_argument("[bioparser::PafParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp:691:24: error: ‘invalid_argument’ is not a member of ‘std’
  691 |             throw std::invalid_argument("[bioparser::PafParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool bioparser::PafParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t, bool)’:
/usr/include/bioparser/bioparser.hpp:714:28: error: ‘invalid_argument’ is not a member of ‘std’
  714 |                 throw std::invalid_argument("[bioparser::PafParser] error: "
      |                            ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In lambda function:
/usr/include/bioparser/bioparser.hpp:839:24: error: ‘invalid_argument’ is not a member of ‘std’
  839 |             throw std::invalid_argument("[bioparser::SamParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp:867:24: error: ‘invalid_argument’ is not a member of ‘std’
  867 |             throw std::invalid_argument("[bioparser::SamParser] error: "
      |                        ^~~~~~~~~~~~~~~~
/usr/include/bioparser/bioparser.hpp: In member function ‘bool bioparser::SamParser<T>::parse(std::vector<std::unique_ptr<T> >&, uint64_t, bool)’:
/usr/include/bioparser/bioparser.hpp:891:28: error: ‘invalid_argument’ is not a member of ‘std’
  891 |                 throw std::invalid_argument("[bioparser::SamParser] error: "
      |                            ^~~~~~~~~~~~~~~~
[ 50%] Building CXX object CMakeFiles/racon.dir/src/overlap.cpp.o
/usr/bin/c++  -DRACON_VERSION=\"v1.4.10\" -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic   -pthread -std=c++11 -o CMakeFiles/racon.dir/src/overlap.cpp.o -c /<<PKGBUILDDIR>>/src/overlap.cpp
make[3]: *** [CMakeFiles/racon_test.dir/build.make:66: CMakeFiles/racon_test.dir/test/racon_test.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
[ 57%] Building CXX object CMakeFiles/racon.dir/src/sequence.cpp.o
/usr/bin/c++  -DRACON_VERSION=\"v1.4.10\" -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic   -pthread -std=c++11 -o CMakeFiles/racon.dir/src/sequence.cpp.o -c /<<PKGBUILDDIR>>/src/sequence.cpp
[ 64%] Building CXX object CMakeFiles/racon.dir/src/window.cpp.o
/usr/bin/c++  -DRACON_VERSION=\"v1.4.10\" -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic   -pthread -std=c++11 -o CMakeFiles/racon.dir/src/window.cpp.o -c /<<PKGBUILDDIR>>/src/window.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:81: CMakeFiles/racon_test.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[ 71%] Linking CXX executable bin/racon
/usr/bin/cmake -E cmake_link_script CMakeFiles/racon.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic  -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/racon.dir/src/main.cpp.o CMakeFiles/racon.dir/src/logger.cpp.o CMakeFiles/racon.dir/src/polisher.cpp.o CMakeFiles/racon.dir/src/overlap.cpp.o CMakeFiles/racon.dir/src/sequence.cpp.o CMakeFiles/racon.dir/src/window.cpp.o  -o bin/racon  -lspoa -lthread_pool -ledlib -lz 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 71%] Built target racon
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:155: 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" returned exit code 2
make: *** [debian/rules:8: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2