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Old 01-25-2011, 03:00 PM   #1
limericksean
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Default tophat 1.2.0 make error

Hi,
I'm having a similar but different issue to previous make errors. I'm getting a make error installing Tophat 1.2.0 on 32-bit linux (ubuntu 10.04). I also got this on tophat 1.1.4 but then I tried the newer version with no luck.

Any help would be appreciated. Thanks,
Sean.

./configure runs fine but the make returns:

sean@sean:~/Downloads/tophat-1.2.0$ make
make all-recursive
make[1]: Entering directory `/home/sean/Downloads/tophat-1.2.0'
Making all in src
make[2]: Entering directory `/home/sean/Downloads/tophat-1.2.0/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/local/include -Wall -march=i686 -O3 -DNDEBUG -I/usr/local/include -I./SeqAn-1.1 -Wall -march=i686 -O3 -DNDEBUG -I/usr/local/include -MT juncs_db.o -MD -MP -MF ".deps/juncs_db.Tpo" -c -o juncs_db.o juncs_db.cpp; \
then mv -f ".deps/juncs_db.Tpo" ".deps/juncs_db.Po"; else rm -f ".deps/juncs_db.Tpo"; exit 1; fi
In file included from juncs_db.cpp:32:
bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
bwt_map.h:680: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
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
make[2]: Leaving directory `/home/sean/Downloads/tophat-1.2.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/sean/Downloads/tophat-1.2.0'
make: *** [all] Error 2
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Old 01-25-2011, 11:27 PM   #2
burt
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Default

I've got the same error.
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Old 01-27-2011, 06:37 AM   #3
natstreet
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same here...anyone spotted the solution/cause?
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Old 01-28-2011, 01:23 PM   #4
ttnguyen
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Location: Ireland

Join Date: Mar 2010
Posts: 41
Default

Something wrong with seqan

Have you tried this way?

Download Seqan1.2 (you may try other versions) at http://www.seqan.de/uploads/media/Seqan_Release_1.2.zip
Then unzip and copy into this directory tophat-1.2.0/src/SeqAn-1.1

This works fine for me in both 32bit and 64bit. Hope Tophat authors could provide a better solution.

Regards,
Nguyen
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Old 04-20-2011, 05:16 AM   #5
nijibabulu
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Location: Vienna, Austria

Join Date: Apr 2011
Posts: 1
Default

This worked for me. Change the line in configure from:
AM_CXXFLAGS="$CXXFLAGS -I./SeqAn-1.1"
to
AM_CXXFLAGS="$CXXFLAGS -I./SeqAn-1.2"
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