Package: berkeley-express Version: 1.5.1-1 Severity: important User: [email protected] Usertags: ftbfs-gcc-6 gcc-6-no-match
This package fails to build with GCC 6. GCC 6 has not been released yet, but it's expected that GCC 6 will become the default compiler for stretch. Note that only the first error is reported; there might be more. You can find a snapshot of GCC 6 in experimental. To build with GCC 6, you can set CC=gcc-6 CXX=g++-6 explicitly. You may be able to find out more about this issue at https://gcc.gnu.org/gcc-6/changes.html > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux ... > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/sequence.cpp.o -c /<<PKGBUILDDIR>>/src/sequence.cpp > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/bundles.cpp.o -c /<<PKGBUILDDIR>>/src/bundles.cpp > [ 94%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/targets.pb.cc.o -c > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/targets.pb.cc > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/c++ > -I/usr/include/bamtools -Wall -O3 -DNDEBUG -o > CMakeFiles/express.dir/alignments.pb.cc.o -c > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/alignments.pb.cc > In file included from /<<PKGBUILDDIR>>/src/main.cpp:42:0: > /<<PKGBUILDDIR>>/src/update_check.h: In function 'bool > get_current_version(char*)': > /<<PKGBUILDDIR>>/src/update_check.h:89:28: warning: argument to 'sizeof' in > 'void bzero(void*, size_t)' call is the same expression as the destination; > did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] > bzero(curr_version, sizeof(curr_version)); > ^ > > /<<PKGBUILDDIR>>/src/targets.cpp: In member function 'double > Target::sample_likelihood(bool, const std::vector<const Target*>*) const': > /<<PKGBUILDDIR>>/src/targets.cpp:116:62: error: no matching function for call > to 'Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const' > double tot_eff_len = cached_effective_length(lib.bias_table); > ^ > > In file included from /<<PKGBUILDDIR>>/src/targets.cpp:10:0: > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: candidate: double > Target::cached_effective_length(bool) const > double cached_effective_length(bool with_bias=true) const; > ^~~~~~~~~~~~~~~~~~~~~~~ > > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: no known conversion for > argument 1 from 'const boost::shared_ptr<BiasBoss>' to 'bool' > /<<PKGBUILDDIR>>/src/targets.cpp:121:77: error: no matching function for call > to 'Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const' > > neighbor->cached_effective_length(lib.bias_table)); > ^ > > In file included from /<<PKGBUILDDIR>>/src/targets.cpp:10:0: > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: candidate: double > Target::cached_effective_length(bool) const > double cached_effective_length(bool with_bias=true) const; > ^~~~~~~~~~~~~~~~~~~~~~~ > > /<<PKGBUILDDIR>>/src/targets.h:399:10: note: no known conversion for > argument 1 from 'const boost::shared_ptr<BiasBoss>' to 'bool' > src/CMakeFiles/express.dir/build.make:225: recipe for target > 'src/CMakeFiles/express.dir/targets.cpp.o' failed > make[3]: *** [src/CMakeFiles/express.dir/targets.cpp.o] Error 1 -- Martin Michlmayr Linux for HPE Helion, Hewlett Packard Enterprise
