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  • Tophat 1.2.0 make error

    Hello everyone,

    I am using UNIX on MAC OS X, and having problems installing Tophat-1.2.0.

    The ./configure part of the installation is working fine. The problems start at the 'make' stage. My problem appears to be with SeqAn. The solution of replacing the SeqAn file with a newer version (see link) does not seem to work for me.

    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    As per the instruction in this link, these are the steps I have taken:

    1) Create a new SeqAn folder and copy new version of SeqAn to it:
    Code:
    cp -r Seqan_Release_1/ tophat-1.2.0/src/SeqAn-1.2/
    2) Replace the line in the configure file to point to new SeqAn location:
    Code:
    AM_CXXFLAGS="$CXXFLAGS -I./SeqAn-1.2"
    3) Run configure specifying BAM library location:
    Code:
    ./configure --prefix=/home/downloads/tophat-1.2.0/ --with-bam=/home/bin/
    4) Run make - and here the errors come:

    Code:
    make  all-recursive
    make[1]: Entering directory `/home/ufaserv1_m/medmabe/downloads/tophat-1.2.0'
    Making all in src
    make[2]: Entering directory `/home/ufaserv1_m/medmabe/downloads/tophat-1.2.0/src'
    if icpc -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -m64 -O3  -DNDEBUG -I/home/ufaserv1_m/medmabe/bin//include -I./SeqAn-1.1 -Wall -m64 -O3  -DNDEBUG -I/home/ufaserv1_m/medmabe/bin//include -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \
    	then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi
    ./SeqAn-1.1/seqan/platform.h(23): error: invalid combination of type specifiers
      typedef int64_t __int64;
                      ^
    
    reads.h(35): remark #981: operands are evaluated in unspecified order
      	bool lengths_equal() { return seq.length() == qual.length(); }
      	                                           ^
    
    reads.h(62): remark #1418: external function definition with no prior declaration
      string DnaString_to_string(const Type& dnaString)
             ^
    
    bwt_map.h(155): remark #981: operands are evaluated in unspecified order
      			if (_cigar.size() != rhs._cigar.size())
      			                  ^
    
    bwt_map.h(156): remark #981: operands are evaluated in unspecified order
      				return _cigar.size() < rhs._cigar.size();
      				                     ^
    
    bwt_map.h(159): remark #981: operands are evaluated in unspecified order
      				if (!(_cigar[i] == rhs._cigar[i]))
      				                ^
    
    bwt_map.h(160): remark #981: operands are evaluated in unspecified order
      					return (_cigar[i].opcode < rhs._cigar[i].opcode || (_cigar[i].opcode == rhs._cigar[i].opcode && _cigar[i].length < rhs._cigar[i].length)); 
      					                         ^
    
    bwt_map.h(160): remark #981: operands are evaluated in unspecified order
      					return (_cigar[i].opcode < rhs._cigar[i].opcode || (_cigar[i].opcode == rhs._cigar[i].opcode && _cigar[i].length < rhs._cigar[i].length)); 
      					                                                                     ^
    
    bwt_map.h(160): remark #981: operands are evaluated in unspecified order
      					return (_cigar[i].opcode < rhs._cigar[i].opcode || (_cigar[i].opcode == rhs._cigar[i].opcode && _cigar[i].length < rhs._cigar[i].length)); 
      					                                                                                                                 ^
    
    bwt_map.h(287): remark #383: value copied to temporary, reference to temporary used
      		_next_id = max(_next_id, (size_t)_id);
      		                         ^
    
    bwt_map.h(333): remark #869: parameter "keep_seqs" was never referenced
      	RefSequenceTable(bool keep_names, bool keep_seqs = false) : 
      	                                       ^
    
    bwt_map.h(355): remark #383: value copied to temporary, reference to temporary used
                      get_id(name, NULL, len);
                             ^
    
    bwt_map.h(339): remark #869: parameter "keep_seqs" was never referenced
                           bool keep_seqs = false) : 
                                ^
    
    bwt_map.h(368): remark #383: value copied to temporary, reference to temporary used
      		_by_id.insert(make_pair(_id, SequenceInfo(_next_id, NULL, NULL, 0)));
      		              ^
    
    bwt_map.h(501): remark #981: operands are evaluated in unspecified order
      			sort(i->second.begin(), i->second.end(), hit_insert_id_lt);
      			                        ^
    
    bwt_map.h(501): remark #981: operands are evaluated in unspecified order
      			sort(i->second.begin(), i->second.end(), hit_insert_id_lt);
      			^
    
    bwt_map.h(691): remark #383: value copied to temporary, reference to temporary used
      					bh.hitfile_rec(bwt_buf);
      					               ^
    
    bwt_map.h(700): remark #383: value copied to temporary, reference to temporary used
      				    bh.seq(seq);
      				           ^
    
    bwt_map.h(714): remark #383: value copied to temporary, reference to temporary used
      				    bh.qual(qual);
      				            ^
    
    reads.cpp(103): remark #981: operands are evaluated in unspecified order
          replace(seq.begin(),seq.end(),'.','N'); //shouldn't really be needed for FASTA files
                              ^
    
    reads.cpp(103): remark #383: value copied to temporary, reference to temporary used
          replace(seq.begin(),seq.end(),'.','N'); //shouldn't really be needed for FASTA files
                                        ^
    
    reads.cpp(103): remark #383: value copied to temporary, reference to temporary used
          replace(seq.begin(),seq.end(),'.','N'); //shouldn't really be needed for FASTA files
                                            ^
    
    reads.cpp(103): remark #981: operands are evaluated in unspecified order
          replace(seq.begin(),seq.end(),'.','N'); //shouldn't really be needed for FASTA files
          ^
    
    reads.cpp(134): remark #383: value copied to temporary, reference to temporary used
      	tokenize(string(fline), " ", integer_qual_values);
      	                        ^
    
    reads.cpp(134): remark #981: operands are evaluated in unspecified order
      	tokenize(string(fline), " ", integer_qual_values);
      	^
    
    reads.cpp(149): remark #981: operands are evaluated in unspecified order
          if ((!color && qual.length()>=seq.length()) || (color && qual.length()+1>=seq.length())) break;
                                      ^
    
    reads.cpp(149): remark #981: operands are evaluated in unspecified order
          if ((!color && qual.length()>=seq.length()) || (color && qual.length()+1>=seq.length())) break;
                                                                                  ^
    
    reads.cpp(152): remark #981: operands are evaluated in unspecified order
        if ((!color && seq.length()!=qual.length()) || (color && seq.length()!=qual.length()+1)) {
                                   ^
    
    reads.cpp(152): remark #981: operands are evaluated in unspecified order
        if ((!color && seq.length()!=qual.length()) || (color && seq.length()!=qual.length()+1)) {
                                                                             ^
    
    reads.cpp(154): remark #981: operands are evaluated in unspecified order
                     qual.length(), seq.length(), alt_name.c_str());
                                    ^
    
    reads.cpp(153): remark #981: operands are evaluated in unspecified order
                 err_exit("Error: qual length (%d) differs from seq length (%d) for fastq record %s!\n",
                 ^
    
    reads.cpp(178): remark #981: operands are evaluated in unspecified order
      	reverse(seq.begin(), seq.end());
      	                     ^
    
    reads.cpp(178): remark #981: operands are evaluated in unspecified order
      	reverse(seq.begin(), seq.end());
      	^
    
    reads.cpp(351): remark #2259: non-pointer conversion from "int" to "char" may lose significant bits
        char base = toupper(bp[0]);
                    ^
    
    reads.cpp(358): remark #2259: non-pointer conversion from "int" to "char" may lose significant bits
            char next = toupper(bp[i]);
                        ^
    
    reads.cpp(376): remark #2259: non-pointer conversion from "int" to "char" may lose significant bits
        char base = toupper(bp[0]);
                    ^
    
    reads.cpp(383): remark #2259: non-pointer conversion from "int" to "char" may lose significant bits
            char next = toupper(bp[i]);
                        ^
    
    reads.cpp(461): remark #2259: non-pointer conversion from "unsigned int" to "char" may lose significant bits
      		  ptr[i_j] = k;
      		           ^
    
    compilation aborted for reads.cpp (code 2)
    make[2]: *** [reads.o] Error 1
    make[2]: Leaving directory `/home/ufaserv1_m/medmabe/downloads/tophat-1.2.0/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/ufaserv1_m/medmabe/downloads/tophat-1.2.0'
    make: *** [all] Error 2
    Thanks for your help.

    Michael

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