macmanes@davinci:/share/paladin$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
bwt.c: In function ‘bwt_invPsi’:
bwt.c:56:2: warning: passing argument 1 of ‘unpackBWTValue’ discards ‘const’ qualifier from pointer target type [enabled by default]
x = unpackBWTValue(bwt, x);
^
bwt.c:28:9: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
ubyte_t unpackBWTValue(bwt_t * passBWT, int passSeqIdx) {
^
bwt.c: In function ‘bwt_occ’:
bwt.c:132:2: warning: passing argument 1 of ‘getOccInterval’ discards ‘const’ qualifier from pointer target type [enabled by default]
n = ((bwtint_t*)(p = getOccInterval(bwt, k)))[c];
^
bwt.c:18:12: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
uint32_t * getOccInterval(bwt_t * passBWT, bwtint_t passIndex) {
^
bwt.c: In function ‘bwt_2occ’:
bwt.c:161:3: warning: passing argument 1 of ‘getOccInterval’ discards ‘const’ qualifier from pointer target type [enabled by default]
n = ((bwtint_t*)(p = getOccInterval(bwt, k)))[c];
^
bwt.c:18:12: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
uint32_t * getOccInterval(bwt_t * passBWT, bwtint_t passIndex) {
^
bwt.c: In function ‘bwt_occ4’:
bwt.c:195:2: warning: passing argument 1 of ‘getOccInterval’ discards ‘const’ qualifier from pointer target type [enabled by default]
p = getOccInterval(bwt, k);
^
bwt.c:18:12: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
uint32_t * getOccInterval(bwt_t * passBWT, bwtint_t passIndex) {
^
bwt.c:204:3: warning: passing argument 1 of ‘unpackBWTValue’ discards ‘const’ qualifier from pointer target type [enabled by default]
cnt[unpackBWTValue(bwt, k/128*128 + supercount)]++;
^
bwt.c:28:9: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
ubyte_t unpackBWTValue(bwt_t * passBWT, int passSeqIdx) {
^
bwt.c:205:3: warning: passing argument 1 of ‘unpackBWTValue’ discards ‘const’ qualifier from pointer target type [enabled by default]
cnt[unpackBWTValue(bwt, k/128*128 + supercount+1)]++;
^
bwt.c:28:9: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
ubyte_t unpackBWTValue(bwt_t * passBWT, int passSeqIdx) {
^
bwt.c:206:3: warning: passing argument 1 of ‘unpackBWTValue’ discards ‘const’ qualifier from pointer target type [enabled by default]
cnt[unpackBWTValue(bwt, k/128*128 + supercount+2)]++;
^
bwt.c:28:9: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
ubyte_t unpackBWTValue(bwt_t * passBWT, int passSeqIdx) {
^
bwt.c:207:3: warning: passing argument 1 of ‘unpackBWTValue’ discards ‘const’ qualifier from pointer target type [enabled by default]
cnt[unpackBWTValue(bwt, k/128*128 + supercount+3)]++;
^
bwt.c:28:9: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
ubyte_t unpackBWTValue(bwt_t * passBWT, int passSeqIdx) {
^
bwt.c:214:3: warning: passing argument 1 of ‘unpackBWTValue’ discards ‘const’ qualifier from pointer target type [enabled by default]
cnt[unpackBWTValue(bwt, k/128*128 + supercount++)]++;
^
bwt.c:28:9: note: expected ‘struct bwt_t *’ but argument is of type ‘const struct bwt_t *’
ubyte_t unpackBWTValue(bwt_t * passBWT, int passSeqIdx) {
^
bwt.c:184:15: warning: unused variable ‘tmp’ [-Wunused-variable]
uint32_t *p, tmp, *end;
^
bwt.c:183:11: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
bwtint_t x;
^
bwt.c: In function ‘bwt_2occ4’:
bwt.c:222:15: warning: variable ‘_l’ set but not used [-Wunused-but-set-variable]
bwtint_t _k, _l;
^
bwt.c:222:11: warning: variable ‘_k’ set but not used [-Wunused-but-set-variable]
bwtint_t _k, _l;
^
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
bntseq.c: In function ‘add1’:
bntseq.c:315:3: warning: array subscript has type ‘char’ [-Wchar-subscripts]
int c = (int) aa_encode_hash[seq->seq.s[i]];
^
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
bwamem.c: In function ‘mem_aln2sam’:
bwamem.c:931:3: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i = qb; i < qe; ++i) str->s[str->l++] = aa_ascii_hash[s->seq[i]];
^
bwamem.c:946:3: warning: array subscript has type ‘char’ [-Wchar-subscripts]
for (i = qe-1; i >= qb; --i) str->s[str->l++] = aa_ascii_hash[s->seq[i]];
^
bwamem.c: In function ‘mem_reg2sam’:
bwamem.c:1037:9: warning: unused variable ‘uniprotEntry’ [-Wunused-variable]
char * uniprotEntry;
^
bwamem.c:1035:12: warning: unused variable ‘parseIdx’ [-Wunused-variable]
int k, l, parseIdx;
^
In file included from bwamem.c:19:0:
bwamem.c: At top level:
uniprot.h:17:22: warning: ‘uniprotEntryLists’ defined but not used [-Wunused-variable]
static UniprotList * uniprotEntryLists = 0;
^
uniprot.h:18:12: warning: ‘uniprotListCount’ defined but not used [-Wunused-variable]
static int uniprotListCount = 0;
^
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
bwtindex.c:23:6: error: conflicting types for ‘packValue’
void packValue(bwt_t * passBWT, int64_t passSeqIdx, bwtint_t passValue) {
^
In file included from bwtindex.c:9:0:
bwtindex.h:10:6: note: previous declaration of ‘packValue’ was here
void packValue(bwt_t * passBWT, int passSeqIdx, bwtint_t passValue);
^
bwtindex.c:31:9: error: conflicting types for ‘unpackValue’
ubyte_t unpackValue(bwt_t * passBWT, int64_t passSeqIdx) {
^
In file included from bwtindex.c:9:0:
bwtindex.h:13:9: note: previous declaration of ‘unpackValue’ was here
ubyte_t unpackValue(bwt_t * passBWT, int passSeqIdx);
^
bwtindex.c: In function ‘command_index’:
bwtindex.c:259:4: warning: implicit declaration of function ‘writeIndexTestProtein’ [-Wimplicit-function-declaration]
writeIndexTestProtein(prefix, proName); break;
^
make: *** [bwtindex.o] Error 1
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