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Old 05-13-2011, 02:44 AM   #1
mabentley86
Junior Member
 
Location: Oxford

Join Date: May 2011
Posts: 4
Default 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.

http://seqanswers.com/forums/showthr...3825#post33825

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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