tophatfusion install problem

[ahmetz]

hey all,

i'm still trying to set my bearings straight with terminal but i get clueless when i get an error when i'm installing something. So, I was installing tophatfusion this morning and configure went without a hitch but make gave an error and exited. Anyone have any ideas what might be the reason in this string of codes? I mean it seems like an error due to prep_reads.o file referencing something not found but i'm not sure how to solve it

thanks

make  all-recursive
Making all in src
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//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
reads.cpp: In function ‘void BWA_decode(const std::string&, const std::string&, const std::string&, std::string&)’:
reads.cpp:506: warning: array subscript has type ‘char’
if gcc -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include  -Wall -arch x86_64 -O3  -DNDEBUG -MT alphabet.o -MD -MP -MF ".deps/alphabet.Tpo" -c -o alphabet.o alphabet.c; \
	then mv -f ".deps/alphabet.Tpo" ".deps/alphabet.Po"; else rm -f ".deps/alphabet.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT bwt_map.o -MD -MP -MF ".deps/bwt_map.Tpo" -c -o bwt_map.o bwt_map.cpp; \
	then mv -f ".deps/bwt_map.Tpo" ".deps/bwt_map.Po"; else rm -f ".deps/bwt_map.Tpo"; exit 1; fi
bwt_map.cpp: In member function ‘virtual bool SplicedBowtieHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)’:
bwt_map.cpp:472: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp:543: warning: comparison between signed and unsigned integer expressions
bwt_map.cpp:549: warning: comparison between signed and unsigned integer expressions
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
	then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT junctions.o -MD -MP -MF ".deps/junctions.Tpo" -c -o junctions.o junctions.cpp; \
	then mv -f ".deps/junctions.Tpo" ".deps/junctions.Po"; else rm -f ".deps/junctions.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT insertions.o -MD -MP -MF ".deps/insertions.Tpo" -c -o insertions.o insertions.cpp; \
	then mv -f ".deps/insertions.Tpo" ".deps/insertions.Po"; else rm -f ".deps/insertions.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT deletions.o -MD -MP -MF ".deps/deletions.Tpo" -c -o deletions.o deletions.cpp; \
	then mv -f ".deps/deletions.Tpo" ".deps/deletions.Po"; else rm -f ".deps/deletions.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT fusions.o -MD -MP -MF ".deps/fusions.Tpo" -c -o fusions.o fusions.cpp; \
	then mv -f ".deps/fusions.Tpo" ".deps/fusions.Po"; else rm -f ".deps/fusions.Tpo"; exit 1; fi
fusions.cpp: In function ‘int difference(const std::string&, const std::string&)’:
fusions.cpp:47: warning: comparison between signed and unsigned integer expressions
fusions.cpp: In function ‘void pair_support(const HitsForRead&, const HitsForRead&, FusionSet&, FusionSet&)’:
fusions.cpp:795: warning: comparison between signed and unsigned integer expressions
fusions.cpp:798: warning: comparison between signed and unsigned integer expressions
fusions.cpp:798: warning: comparison between signed and unsigned integer expressions
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT align_status.o -MD -MP -MF ".deps/align_status.Tpo" -c -o align_status.o align_status.cpp; \
	then mv -f ".deps/align_status.Tpo" ".deps/align_status.Po"; else rm -f ".deps/align_status.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT fragments.o -MD -MP -MF ".deps/fragments.Tpo" -c -o fragments.o fragments.cpp; \
	then mv -f ".deps/fragments.Tpo" ".deps/fragments.Po"; else rm -f ".deps/fragments.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT tokenize.o -MD -MP -MF ".deps/tokenize.Tpo" -c -o tokenize.o tokenize.cpp; \
	then mv -f ".deps/tokenize.Tpo" ".deps/tokenize.Po"; else rm -f ".deps/tokenize.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT inserts.o -MD -MP -MF ".deps/inserts.Tpo" -c -o inserts.o inserts.cpp; \
	then mv -f ".deps/inserts.Tpo" ".deps/inserts.Po"; else rm -f ".deps/inserts.Tpo"; exit 1; fi
rm -f libtophat.a
ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o 
ranlib libtophat.a
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT GBase.o -MD -MP -MF ".deps/GBase.Tpo" -c -o GBase.o GBase.cpp; \
	then mv -f ".deps/GBase.Tpo" ".deps/GBase.Po"; else rm -f ".deps/GBase.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT codons.o -MD -MP -MF ".deps/codons.Tpo" -c -o codons.o codons.cpp; \
	then mv -f ".deps/codons.Tpo" ".deps/codons.Po"; else rm -f ".deps/codons.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT gdna.o -MD -MP -MF ".deps/gdna.Tpo" -c -o gdna.o gdna.cpp; \
	then mv -f ".deps/gdna.Tpo" ".deps/gdna.Po"; else rm -f ".deps/gdna.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT GStr.o -MD -MP -MF ".deps/GStr.Tpo" -c -o GStr.o GStr.cpp; \
	then mv -f ".deps/GStr.Tpo" ".deps/GStr.Po"; else rm -f ".deps/GStr.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT GFaSeqGet.o -MD -MP -MF ".deps/GFaSeqGet.Tpo" -c -o GFaSeqGet.o GFaSeqGet.cpp; \
	then mv -f ".deps/GFaSeqGet.Tpo" ".deps/GFaSeqGet.Po"; else rm -f ".deps/GFaSeqGet.Tpo"; exit 1; fi
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT gff.o -MD -MP -MF ".deps/gff.Tpo" -c -o gff.o gff.cpp; \
	then mv -f ".deps/gff.Tpo" ".deps/gff.Po"; else rm -f ".deps/gff.Tpo"; exit 1; fi
rm -f libgc.a
ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o 
ranlib libgc.a
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/include -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -MT prep_reads.o -MD -MP -MF ".deps/prep_reads.Tpo" -c -o prep_reads.o prep_reads.cpp; \
	then mv -f ".deps/prep_reads.Tpo" ".deps/prep_reads.Po"; else rm -f ".deps/prep_reads.Tpo"; exit 1; fi
g++ -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include -I./SeqAn-1.2 -Wall -arch x86_64 -O3  -DNDEBUG -I/Users/zehira/local/bin/bam_tophat//include  -L/usr/lib -o prep_reads -L/Users/zehira/local/bin/bam_tophat//lib prep_reads.o ../src/libtophat.a -lbam -lz -lz 
Undefined symbols for architecture x86_64:
  "_solToPhred", referenced from:
      charToPhred33(char, bool, bool)in prep_reads.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [prep_reads] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

[dpryan]

use the binary?

I'm assuming that you're not familiar with C++, so is there a reason you're not just using the binary?

[Jon_Keats]

Have you installed boost? The error related to x86_64 is likely due to a boost configuration issue. Check out my intro thread, on page 3 there is an instruction set for tophat that worked when I installed tophat-fusion.

[ahmetz]

@dpryan: yes, I'm not familiar with C++, however, I thought I was installing from the binaries. I mean, they only have one source on the website and it's not precompiled

@Jon_Keats: I have the boost library installed - I can use cufflinks just fine. and your intro thread is open 24/7 on a tab on firefox. you have no idea how helpful that thread is for a biologist who's trying to pretend to be a bioinformatician. i've even set up my own pipeline using yours as a guide.

[dpryan]

There are binaries

Linux: http://tophat-fusion.sourceforge.net...1.0-bin.tar.gz
OS X: https://"http://tophat-fusion.source..._x86_64.tar.gz
Those were listed under releases.

[ahmetz]

@drpryan: thanks for saving my life. i did not think about checking the sourceforge page at all and had assumed that it was only the binaries they hosted. just started a tophat-fusion run and seems like things are working so far. thanks again!