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  • Problem installing tophat

    make all-recursive
    make[1]: Entering directory `/home/tophat-2.0.5'
    Making all in src
    make[2]: Entering directory `/home/tophat-2.0.5/src'
    if g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/include -I/usr/local/include -I./SeqAn-1.3 -MT tophat_reports.o -MD -MP -MF ".deps/tophat_reports.Tpo" -c -o tophat_reports.o tophat_reports.cpp; \
    then mv -f ".deps/tophat_reports.Tpo" ".deps/tophat_reports.Po"; else rm -f ".deps/tophat_reports.Tpo"; exit 1; fi
    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]
    tophat_reports.cpp: At global scope:
    tophat_reports.cpp:121:21: error: ‘boost::random::mt19937’ has not been declared
    tophat_reports.cpp: In function ‘void read_best_alignments(const HitsForRead&, HitsForRead&, const JunctionSet&, const JunctionSet&, const InsertionSet&, const DeletionSet&, const FusionSet&, const Coverage&, bool, int*)’:
    tophat_reports.cpp:194:34: error: ‘* rng’ cannot be used as a function
    tophat_reports.cpp: At global scope:
    tophat_reports.cpp:316:21: error: ‘boost::random::mt19937’ has not been declared
    tophat_reports.cpp: In function ‘void pair_best_alignments(const HitsForRead&, const HitsForRead&, InsertAlignmentGrade&, std::vector<std:air<BowtieHit, BowtieHit> >&, const JunctionSet&, const JunctionSet&, const InsertionSet&, const DeletionSet&, const FusionSet&, const Coverage&, bool, int*)’:
    tophat_reports.cpp:467:34: error: ‘* rng’ cannot be used as a function
    tophat_reports.cpp: At global scope:
    tophat_reports.cpp:875:21: error: ‘boost::random::mt19937’ has not been declared
    tophat_reports.cpp: In function ‘void print_sam_for_single(const RefSequenceTable&, const HitsForRead&, FragmentType, const string&, GBamWriter&, int&)’:
    tophat_reports.cpp:892:24: error: ‘rng’ cannot be used as a function
    tophat_reports.cpp: At global scope:
    tophat_reports.cpp:918:19: error: ‘boost::random::mt19937’ has not been declared
    tophat_reports.cpp: In function ‘void print_sam_for_pair(const RefSequenceTable&, const std::vector<std:air<BowtieHit, BowtieHit> >&, const InsertAlignmentGrade&, GBamWriter&, const string&, const string&, int&, uint64_t, uint64_t)’:
    tophat_reports.cpp:941:24: error: ‘rng’ cannot be used as a function
    tophat_reports.cpp: At global scope:
    tophat_reports.cpp:2215:3: error: ‘mt19937’ in namespace ‘boost::random’ does not name a type
    tophat_reports.cpp: In member function ‘void ReportWorker::write_singleton_alignments(uint64_t, HitsForRead&, ReadStream&, GBamWriter&, GBamWriter&, FragmentType)’:
    tophat_reports.cpp:1942:20: error: ‘rng’ was not declared in this scope
    tophat_reports.cpp: In member function ‘void ReportWorker:perator()()’:
    tophat_reports.cpp:1968:5: error: ‘rng’ was not declared in this scope
    coverage.h: At global scope:
    coverage.h:24:20: warning: ‘cov_max_value’ defined but not used [-Wunused-variable]
    coverage.h:25:20: warning: ‘cov_min_value’ defined but not used [-Wunused-variable]
    make[2]: *** [tophat_reports.o] Error 1
    make[2]: Leaving directory `/home/tophat-2.0.5/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/tophat-2.0.5'
    make: *** [all] Error 2


    Have been trying to install tophat for the past one week and now im completely fed up with this bug eyed software, would be really helpful if someone could shed some light on this problem

  • #2
    this is probably unhelpful but really basic questions to start:

    are you unable to use the binaries available?

    also, did you successfully install the boost and samtools packages first? I also had trouble installing tophat; i no longer remember the error but it was actually a problem installing samtools, not tophat. I see something that looks like a boost error in your output?

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