[Debian-med-packaging] Bug#831208: dindel: FTBFS with GCC 6: DInDel.hpp:145:229: error: template argument 1 is invalid
Lucas Nussbaum
lucas at debian.org
Thu Jul 14 06:53:24 UTC 2016
Source: dindel
Version: 1.01+dfsg-1
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
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.
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