Good morning,
I am having trouble with 'making' bwa. Below I posted my code and my error messages. Any help would be much appreciated.
My commands:
#gets the newest version from sourceforge
wget http://sourceforge.net/projects/bio-...r.bz2/download -O bwa.tar.bz2
#unpacks the tarball
tar -xjf bwa.tar.bz2
cd bwa-0.7.3a
#makes bwa
make
My errors:
jmwhitha@Linux-OptiPlex-755:~/bwa-0.7.3a$ make
gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD ksw.c -o ksw.o
In file included from ksw.c:28:0:
/usr/lib/gcc/i686-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
ksw.c:44:2: error: unknown type name ‘__m128i’
ksw.c: In function ‘ksw_qinit’:
ksw.c:67:11: error: ‘__m128i’ undeclared (first use in this function)
ksw.c:67:11: note: each undeclared identifier is reported only once for each function it appears in
ksw.c:67:19: error: expected expression before ‘)’ token
ksw.c: In function ‘ksw_u8’:
ksw.c:110:2: error: unknown type name ‘__m128i’
ksw.c:126:2: warning: implicit declaration of function ‘_mm_set1_epi32’ [-Wimplicit-function-declaration]
ksw.c:127:2: warning: implicit declaration of function ‘_mm_set1_epi8’ [-Wimplicit-function-declaration]
ksw.c:133:3: warning: implicit declaration of function ‘_mm_store_si128’ [-Wimplicit-function-declaration]
ksw.c:140:3: error: unknown type name ‘__m128i’
ksw.c:141:3: warning: implicit declaration of function ‘_mm_load_si128’ [-Wimplicit-function-declaration]
ksw.c:142:3: warning: implicit declaration of function ‘_mm_slli_si128’ [-Wimplicit-function-declaration]
ksw.c:150:4: warning: implicit declaration of function ‘_mm_adds_epu8’ [-Wimplicit-function-declaration]
ksw.c:151:4: warning: implicit declaration of function ‘_mm_subs_epu8’ [-Wimplicit-function-declaration]
ksw.c:153:4: warning: implicit declaration of function ‘_mm_max_epu8’ [-Wimplicit-function-declaration]
ksw.c:177:5: warning: implicit declaration of function ‘_mm_movemask_epi8’ [-Wimplicit-function-declaration]
ksw.c:177:5: warning: implicit declaration of function ‘_mm_cmpeq_epi8’ [-Wimplicit-function-declaration]
ksw.c:183:3: warning: implicit declaration of function ‘_mm_srli_si128’ [-Wimplicit-function-declaration]
ksw.c:183:3: warning: implicit declaration of function ‘_mm_extract_epi16’ [-Wimplicit-function-declaration]
ksw.c: In function ‘ksw_i16’:
ksw.c:227:2: error: unknown type name ‘__m128i’
ksw.c:243:2: warning: implicit declaration of function ‘_mm_set1_epi16’ [-Wimplicit-function-declaration]
ksw.c:255:3: error: unknown type name ‘__m128i’
ksw.c:259:4: warning: implicit declaration of function ‘_mm_adds_epi16’ [-Wimplicit-function-declaration]
ksw.c:261:4: warning: implicit declaration of function ‘_mm_max_epi16’ [-Wimplicit-function-declaration]
ksw.c:265:4: warning: implicit declaration of function ‘_mm_subs_epu16’ [-Wimplicit-function-declaration]
ksw.c:281:5: warning: implicit declaration of function ‘_mm_cmpgt_epi16’ [-Wimplicit-function-declaration]
make: *** [ksw.o] Error 1
Thank you and God bless,
Jason
I am having trouble with 'making' bwa. Below I posted my code and my error messages. Any help would be much appreciated.
My commands:
#gets the newest version from sourceforge
wget http://sourceforge.net/projects/bio-...r.bz2/download -O bwa.tar.bz2
#unpacks the tarball
tar -xjf bwa.tar.bz2
cd bwa-0.7.3a
#makes bwa
make
My errors:
jmwhitha@Linux-OptiPlex-755:~/bwa-0.7.3a$ make
gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD ksw.c -o ksw.o
In file included from ksw.c:28:0:
/usr/lib/gcc/i686-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
ksw.c:44:2: error: unknown type name ‘__m128i’
ksw.c: In function ‘ksw_qinit’:
ksw.c:67:11: error: ‘__m128i’ undeclared (first use in this function)
ksw.c:67:11: note: each undeclared identifier is reported only once for each function it appears in
ksw.c:67:19: error: expected expression before ‘)’ token
ksw.c: In function ‘ksw_u8’:
ksw.c:110:2: error: unknown type name ‘__m128i’
ksw.c:126:2: warning: implicit declaration of function ‘_mm_set1_epi32’ [-Wimplicit-function-declaration]
ksw.c:127:2: warning: implicit declaration of function ‘_mm_set1_epi8’ [-Wimplicit-function-declaration]
ksw.c:133:3: warning: implicit declaration of function ‘_mm_store_si128’ [-Wimplicit-function-declaration]
ksw.c:140:3: error: unknown type name ‘__m128i’
ksw.c:141:3: warning: implicit declaration of function ‘_mm_load_si128’ [-Wimplicit-function-declaration]
ksw.c:142:3: warning: implicit declaration of function ‘_mm_slli_si128’ [-Wimplicit-function-declaration]
ksw.c:150:4: warning: implicit declaration of function ‘_mm_adds_epu8’ [-Wimplicit-function-declaration]
ksw.c:151:4: warning: implicit declaration of function ‘_mm_subs_epu8’ [-Wimplicit-function-declaration]
ksw.c:153:4: warning: implicit declaration of function ‘_mm_max_epu8’ [-Wimplicit-function-declaration]
ksw.c:177:5: warning: implicit declaration of function ‘_mm_movemask_epi8’ [-Wimplicit-function-declaration]
ksw.c:177:5: warning: implicit declaration of function ‘_mm_cmpeq_epi8’ [-Wimplicit-function-declaration]
ksw.c:183:3: warning: implicit declaration of function ‘_mm_srli_si128’ [-Wimplicit-function-declaration]
ksw.c:183:3: warning: implicit declaration of function ‘_mm_extract_epi16’ [-Wimplicit-function-declaration]
ksw.c: In function ‘ksw_i16’:
ksw.c:227:2: error: unknown type name ‘__m128i’
ksw.c:243:2: warning: implicit declaration of function ‘_mm_set1_epi16’ [-Wimplicit-function-declaration]
ksw.c:255:3: error: unknown type name ‘__m128i’
ksw.c:259:4: warning: implicit declaration of function ‘_mm_adds_epi16’ [-Wimplicit-function-declaration]
ksw.c:261:4: warning: implicit declaration of function ‘_mm_max_epi16’ [-Wimplicit-function-declaration]
ksw.c:265:4: warning: implicit declaration of function ‘_mm_subs_epu16’ [-Wimplicit-function-declaration]
ksw.c:281:5: warning: implicit declaration of function ‘_mm_cmpgt_epi16’ [-Wimplicit-function-declaration]
make: *** [ksw.o] Error 1
Thank you and God bless,
Jason
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