Package: tophat Version: 2.1.0+dfsg-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 ... > g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall > -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG > -I./samtools-0.1.18 -pthread -I/usr/include -c -o tophat_reports.o > tophat_reports.cpp > In file included from tophat_reports.cpp:36:0: > common.h: In member function 'void GBamWriter::write(bam1_t*, int64_t)': > common.h:579:14: warning: variable 'pre_block_offs' set but not used > [-Wunused-but-set-variable] > int pre_block_offs=0; //but before this write() > ^~~~~~~~~~~~~~ > > tophat_reports.cpp: In member function 'void > ReportWorker::write_singleton_alignments(uint64_t, HitsForRead&, ReadStream&, > GBamWriter&, FragmentType, GetReadProc*, QReadData)': > tophat_reports.cpp:2292:8: warning: variable 'map_code' set but not used > [-Wunused-but-set-variable] > char map_code=0; > ^~~~~~~~ > > tophat_reports.cpp: In function 'void driver(const string&, std::istream&, > const std::vector<std::__cxx11::basic_string<char> >&, const string&, const > std::vector<std::__cxx11::basic_string<char> >&, const string&, FILE*, FILE*, > FILE*, FILE*)': > tophat_reports.cpp:2707:128: error: no matching function for call to > 'make_pair(Junction, JunctionStats&)' > gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, > left_coord, right_coord, antisense), junction_stat)); > > ^ > > In file included from /usr/include/c++/6/bits/stl_algobase.h:64:0, > from /usr/include/c++/6/vector:60, > from tophat_reports.cpp:20: > /usr/include/c++/6/bits/stl_pair.h:406:5: note: candidate: template<class > _T1, class _T2> constexpr std::pair<typename > std::__decay_and_strip<_Tp>::__type, typename > std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) > make_pair(_T1&& __x, _T2&& __y) > ^~~~~~~~~ > > /usr/include/c++/6/bits/stl_pair.h:406:5: note: template argument > deduction/substitution failed: > tophat_reports.cpp:2707:128: note: cannot convert 'junction_stat' (type > 'JunctionStats') to type 'JunctionStats&&' > gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, > left_coord, right_coord, antisense), junction_stat)); > > ^ > > Makefile:1453: recipe for target 'tophat_reports.o' failed > make[3]: *** [tophat_reports.o] Error 1 -- Martin Michlmayr Linux for HPE Helion, Hewlett Packard Enterprise
