Source: dindel Version: 1.01+dfsg-1 Severity: serious Tags: stretch sid User: [email protected] Usertags: qa-ftbfs-20160713 qa-ftbfs Justification: FTBFS with GCC 6 on amd64
Hi, During a rebuild of all packages in sid using the gcc-defaults package available in experimental to make GCC default to version 6, your package failed to build on amd64. For more information about GCC 6 and Stretch, see: - https://wiki.debian.org/GCC6 - https://lists.debian.org/debian-devel-announce/2016/06/msg00007.html Relevant part (hopefully): > g++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security > -I/usr/include/samtools -I/usr/include/seqan -I./ -Wno-deprecated -O3 > -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL -c > -o DInDel.o DInDel.cpp > In file included from DInDel.cpp:29:0: > DInDel.hpp:145:229: error: template argument 1 is invalid > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:231: error: template argument 2 is invalid > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.hpp:145:231: error: template argument 4 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:231: error: template argument 2 is invalid > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.hpp:145:231: error: template argument 4 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:229: error: template argument 1 is invalid > DInDel.hpp:145:229: error: template argument 2 is invalid > DInDel.hpp:145:231: error: template argument 2 is invalid > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.hpp:145:231: error: template argument 4 is invalid > DInDel.hpp:145:175: error: 'map' is not a type > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^~~ > DInDel.hpp:145:179: error: expected ',' or '...' before '<' token > void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, > const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, > vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, > double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & > glfOutput); > > > ^ > DInDel.cpp: In member function 'void > DetInDel::empiricalDistributionMethod(int, const std::vector<Read>&, > uint32_t, uint32_t, uint32_t, const AlignedCandidates&, OutputData&, > OutputData&)': > DInDel.cpp:413:59: error: template argument 1 is invalid > map <int, vector<tuple<AlignedVariant, double, double> > > posteriors; > ^ > DInDel.cpp:413:59: error: template argument 2 is invalid > DInDel.cpp:413:61: error: template argument 2 is invalid > map <int, vector<tuple<AlignedVariant, double, double> > > posteriors; > ^ > DInDel.cpp:413:61: error: template argument 4 is invalid > DInDel.cpp:544:59: error: template argument 1 is invalid > map <int, vector<tuple<AlignedVariant, double, double> > > posteriors; > ^ > DInDel.cpp:544:59: error: template argument 2 is invalid > DInDel.cpp:544:61: error: template argument 2 is invalid > map <int, vector<tuple<AlignedVariant, double, double> > > posteriors; > ^ > DInDel.cpp:544:61: error: template argument 4 is invalid > DInDel.cpp:525:31: warning: ignoring return value of 'int system(const > char*)', declared with attribute warn_unused_result [-Wunused-result] > system(cmd.str().c_str()); > ^ > DInDel.cpp:629:31: warning: ignoring return value of 'int system(const > char*)', declared with attribute warn_unused_result [-Wunused-result] > system(cmd.str().c_str()); > ^ > make[1]: *** [DInDel.o] Error 1 The full build log is available from: http://people.debian.org/~lucas/logs/2016/07/13/dindel_1.01+dfsg-1_unstable_gcc6.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
