Question: Building Tophat Release 1.2.0Beta
0
gravatar for Laurent Gautier
8.0 years ago by
Laurent Gautier810 wrote:

Hi,

We are having trouble to build TopHat from source, and do not know where to report the issue (the email address given on the site did not return any answer)

The configure step appears all fine:

-- tophat 1.2.0 Configuration Results --
C compiler:          gcc -Wall -m64 -O3  -DNDEBUG
C++ compiler:        g++ -Wall -m64 -O3  -DNDEBUG -I/usr/local/include
GCC version:         gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
Host System type:    x86_64-unknown-linux-gnu

but running make ends with:

In file included from ./SeqAn-1.1/seqan/sequence.h:51,
                  from juncs_db.cpp:26:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::clear(seqan::String<TValue, TSpec>&) [with TValue = char, TSpec = seqan::CStyle]’:
./SeqAn-1.1/seqan/sequence/string_cstyle.h:492:   instantiated from ‘static void seqan::_Assign_String_2_StringArray<TExpand, true>::assign_(seqan::String<char, seqan::CStyle>&, seqan::String<char, TSourceSpec>&) [with TSourceSpec = seqan::Alloc<void>, TExpand = const seqan::Tag<seqan::TagExact_>]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:522:   instantiated from ‘void seqan::assign(seqan::String<TTargetValue, seqan::CStyle>&, seqan::String<TValue, TSpec>&, seqan::Tag<TTag>) [with TValue = char, TSourceSpec = seqan::Alloc<void>, TExpand = seqan::TagExact_]’
./SeqAn-1.1/seqan/sequence/string_base.h:737:   instantiated from ‘void seqan::assign(seqan::String<TValue, TSpec>&, TSource&) [with TTargetValue = char, TTargetSpec = seqan::CStyle, TSource = seqan::String<char, seqan::Alloc<void> >]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:97:   instantiated from ‘seqan::String<TTargetValue, seqan::CStyle>::String(TString&) [with TString = seqan::String<char, seqan::Alloc<void> >, TValue = char]’
./SeqAn-1.1/seqan/sequence/string_cstyle.h:798:   instantiated from ‘typename seqan::Value<T, 0>::Type* seqan::toCString(T&) [with T = seqan::String<char, seqan::Alloc<void> >]’
juncs_db.cpp:327:   instantiated from here
./SeqAn-1.1/seqan/sequence/string_base.h:207: error: no matching function for call to ‘_setLength(seqan::String<char, seqan::CStyle>&, int)’
make[2]: *** [juncs_db.o] Error 1
tophat • 1.8k views
ADD COMMENTlink written 8.0 years ago by Laurent Gautier810
3
gravatar for Brad Chapman
8.0 years ago by
Brad Chapman9.4k
Boston, MA
Brad Chapman9.4k wrote:

Ran into this one as well and SeqAnswers helped out:

http://seqanswers.com/forums/showthread.php?t=9082

Remove the included SeqAn in src/SeqAn-1.1 and replace it with the latest release:

http://www.seqan.de/uploads/media/Seqan_Release_1.2.zip

There is an automated build of this as part of CloudBioLinux:

https://github.com/chapmanb/bcbb/blob/master/ec2/biolinux/custom/bio_nextgen.py

so you could install with:

fab -f fabfile.py install_custom:tophat -H localhost
ADD COMMENTlink written 8.0 years ago by Brad Chapman9.4k

Thanks. It does build with Seqan 1.2. Somehow did not find the seqanswers thread when looking for earlier reports of the issue. Reporting problems to TopHat developpers also appears difficult to others.

ADD REPLYlink written 8.0 years ago by Laurent Gautier810
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