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Old 06-18-2012, 08:18 AM   #1
elfuser
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Location: Toronto, ON

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Posts: 16
Default Installing bwa in Fedora 10

Im trying to install BWA in a Fedora 10 64 bit machine
and I run the following commands:
Code:
tar xvjf bwa-0.6.1.tar.bz2
make
I get the following error:
Code:
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   QSufSort.c -o QSufSort.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwt_gen.c -o bwt_gen.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   utils.c -o utils.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwt.c -o bwt.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtio.c -o bwtio.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtaln.c -o bwtaln.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtgap.c -o bwtgap.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   is.c -o is.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bntseq.c -o bntseq.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtmisc.c -o bwtmisc.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwtindex.c -o bwtindex.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   ksw.c -o ksw.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   stdaln.c -o stdaln.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   simple_dp.c -o simple_dp.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD   bwaseqio.c -o bwaseqio.o
In file included from bwtaln.h:6,
                 from bwaseqio.c:4:
bwt.h:61: error: expected specifier-qualifier-list before ‘size_t’
make: *** [bwaseqio.o] Error 1
Any clues?
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Old 06-18-2012, 08:45 AM   #2
Richard Finney
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Default

Check this out : http://stackoverflow.com/questions/2...-c-header-file

Maybe you need to include this line:
#include <stddef.h>
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Old 06-18-2012, 09:11 AM   #3
elfuser
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Default

In which file should I make this change.
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Old 06-18-2012, 10:02 AM   #4
elfuser
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Posts: 16
Default

I changed the header in the file bwaseqio.c and it worked! Thanks
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