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Old 05-10-2009, 09:56 PM   #1
mabry
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Location: Tokyo

Join Date: May 2009
Posts: 2
Default BWA compilation error

I'm trying to complie BWA on my Linux (Fedora 9, x86_64) box from bwa-0.6.4 source. But, when I type 'make',

make[1]: Entering directory `/usr/local/bwa-0.4.6'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/usr/local/bwa-0.4.6'
make[1]: Entering directory `/usr/local/bwa-0.4.6/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
make[1]: Leaving directory `/usr/local/bwa-0.4.6/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwt.c -o bwt.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwtio.c -o bwtio.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
bwtaln.c: In function ‘bwa_aln’:
bwtaln.c:227: warning: implicit declaration of function ‘getopt’
bwtaln.c:230: error: ‘optarg’ undeclared (first use in this function)
bwtaln.c:230: error: (Each undeclared identifier is reported only once
bwtaln.c:230: error: for each function it appears in.)
bwtaln.c:256: error: ‘optind’ undeclared (first use in this function)
make: *** [bwtaln.o] Error 1

Any suggestions would be appreciated.
Thanks.
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Old 05-12-2009, 04:30 AM   #2
lh3
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Location: Boston

Join Date: Feb 2008
Posts: 693
Default

add this line to the beginning of bwtaln.c:

#include <unistd.h>
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Old 05-12-2009, 05:16 AM   #3
mabry
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Location: Tokyo

Join Date: May 2009
Posts: 2
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Hi lh3,

I could successfully compile bwa with the modifications of the additional two files, bwape.c and bwase.c, in same way.
Thank you so much for your help.
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