Question: Tophat on Debian Jessie installlation problem
1
gravatar for Pommy
4.5 years ago by
Pommy10
Pommy10 wrote:

I have a problem building tophat 2.1.0 on Debian jessie. Running configure does not seem to produce errors (see below) but running make causes fails with

#some output ommited here

Makefile:1347: recipe for target 'reads.o' failed
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory '/home/pommy/inst/tophat-2.1.0/src'
Makefile:313: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/pommy/inst/tophat-2.1.0'
Makefile:253: recipe for target 'all' failed
make: *** [all] Error 2

 

Here are the configuration results

- tophat 2.1.0 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3  -DNDEBUG -I./samtools-0.1.18 -pthread -I/home/pommy/include -I./SeqAn-1.3
  Linker flags:        -L./samtools-0.1.18 -L/home/pommy/lib
  BOOST libraries:     -lboost_thread -lboost_system
  GCC version:         gcc (Debian 4.9.2-10) 4.9.2
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /home/pommy
  Install eprefix:     ${prefix}

 


 

rna-seq software error • 1.9k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 4.5 years ago by Pommy10
2

I think that it is probably related to TopHat's issue 7 on Github. On Debian, we solved it by building TopHat with a more recent version of SeqAn. I am preparing a backport for Jessie and will let you know when it is available.

ADD REPLYlink written 4.4 years ago by Charles Plessy2.7k

Backport done (see my answer below)... and I just saw that TopHat 2.1.1 was released in the meantime !

ADD REPLYlink written 4.4 years ago by Charles Plessy2.7k

The real error is in the omitted output. Try to locate it to find out what fails.

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by Jean-Karim Heriche22k

Ok here is the whole part corresponding to reads.o compilation. I don't understand where is the actual error

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.5 years ago by Pommy10

The cause is on the line that has the word 'error'. It could be an issue with the version of GCC you're using for compiling. In my experience, newer versions tend to be stricter and turn what was warnings for older versions into errors. Otherwise, it looks like it could be a bug in the software. You may want to contact the developers.

ADD REPLYlink written 4.5 years ago by Jean-Karim Heriche22k
1
gravatar for blaise.li__biostars
4.4 years ago by
France
blaise.li__biostars50 wrote:

Solution found here: https://github.com/infphilo/tophat/pull/13

 

I managed compiling a fork that uses a newer SeqAn version:


git clone https://github.com/wookietreiber/tophat.git
cd tophat
git checkout update-seqan
./bootstrap
./configure <insert your options here>
make
make install

 


(See also https://groups.google.com/forum/#!topic/tuxedo-tools-users/M7Z9zLuu8o4)

 
ADD COMMENTlink written 4.4 years ago by blaise.li__biostars50
0
gravatar for blaise.li__biostars
4.4 years ago by
France
blaise.li__biostars50 wrote:

For the record, I confirm the error for me on Debian:

 

                                                           ^
In file included from ./SeqAn-1.3/seqan/file.h:56:0,
                 from ./SeqAn-1.3/seqan/score/score_matrix.h:40,
                 from ./SeqAn-1.3/seqan/score.h:48,
                 from ./SeqAn-1.3/seqan/find.h:45,
                 from reads.cpp:22:
./SeqAn-1.3/seqan/file/file_generated_forwards.h: At global scope:
./SeqAn-1.3/seqan/file/file_generated_forwards.h:927:66: error: invalid abstract return type 'seqan::FileFormat<TFile, TData, TMeta, void>'
 template <typename TFile, typename TData, typename TMeta> inline FileFormat<TFile, TData, TMeta, void> guessFileFormat(TFile & file, TData & data);        // "projects/library/seqan/file/file_format_guess.h"(65)
                                                                  ^

No problem compiling the same program on Ubuntu 14.04.

 

On Debian, gcc version is "(Debian 4.9.2-10) 4.9.2"

On Ubuntu, it is "(Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4"

 

ADD COMMENTlink written 4.4 years ago by blaise.li__biostars50
0
gravatar for Charles Plessy
4.4 years ago by
Charles Plessy2.7k
Japan
Charles Plessy2.7k wrote:

For everybody's convenience, there is now a backport of tophat 2.1.0 for Jessie.

ADD COMMENTlink written 4.4 years ago by Charles Plessy2.7k
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