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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.
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:
2) Replace the line in the configure file to point to new SeqAn location:
3) Run configure specifying BAM library location:
4) Run make - and here the errors come:
Thanks for your help.
Michael
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.
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/
Code:
AM_CXXFLAGS="$CXXFLAGS -I./SeqAn-1.2"
Code:
./configure --prefix=/home/downloads/tophat-1.2.0/ --with-bam=/home/bin/
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
Michael