>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.12.2.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_Rsamtools.c -o R_init_Rsamtools.o
In file included from R_init_Rsamtools.c:3:
In file included from ./bamfile.h:5:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from R_init_Rsamtools.c:4:
In file included from ./bcffile.h:5:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
In file included from R_init_Rsamtools.c:6:
In file included from ./tabixfile.h:5:
In file included from ./tabix/tabix.h:32:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c as_bam.c -o as_bam.o
In file included from as_bam.c:1:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bamfile.c -o bamfile.o
In file included from bamfile.c:1:
In file included from ./bamfile.h:5:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
bamfile.c:75:23: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
bfile->pos0 = bam_tell(bfile->file->x.bam);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bcffile.c -o bcffile.o
In file included from bcffile.c:3:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
In file included from bcffile.c:4:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
bcffile.c:323:43: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *txt = (char *) R_alloc(hdr->l_txt, sizeof(char));
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜
bcffile.c:356:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int pos = strlen(bcf1->ref);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bcffile.c:438:32: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
bgzf_seek(bcf->fp, off, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ^˜˜
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c encode.c -o encode.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fafile.c -o fafile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io_sam.c -o io_sam.o
In file included from io_sam.c:1:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
In file included from io_sam.c:2:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
io_sam.c:77:17: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
magic_len = bam_read(bfile, buf, 4);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:58:33: note: expanded from macro 'bam_read'
#define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:102:24: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
bd->CIGAR_BUF_SZ = cigar_buf_sz;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:122:24: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
bd->keep_flag[0] = INTEGER(flag)[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:123:24: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
bd->keep_flag[1] = INTEGER(flag)[1];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:124:22: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
bd->cigar_flag = LOGICAL(isSimpleCigar)[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:208:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->flag = Realloc(sbd->flag, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:211:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->rname = Realloc(sbd->rname, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:214:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->strand = Realloc(sbd->strand, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:217:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->pos = Realloc(sbd->pos, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:220:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->qwidth = Realloc(sbd->qwidth, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:223:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->mapq = Realloc(sbd->mapq, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:226:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->mrnm = Realloc(sbd->mrnm, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:229:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->mpos = Realloc(sbd->mpos, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:232:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->isize = Realloc(sbd->isize, len, int);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:235:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->qname = Realloc(sbd->qname, len, char *);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:238:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->cigar = Realloc(sbd->cigar, len, const char *);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:241:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->seq = Realloc(sbd->seq, len, const char *);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:244:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sbd->qual = Realloc(sbd->qual, len, const char *);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
io_sam.c:361:36: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
const uint32_t len = bam->core.l_qseq;
˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
io_sam.c:367:31: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
_reverseComplement(s, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
io_sam.c:374:36: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
const uint32_t len = bam->core.l_qseq;
˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
io_sam.c:378:24: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
s[i] = bamq[i] + 33;
˜ ˜˜˜˜˜˜˜˜^˜˜˜
io_sam.c:380:21: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
_reverse(s, len);
˜˜˜˜˜˜˜˜ ^˜˜
io_sam.c:417:20: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE was = TYPEOF(tag);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
io_sam.c:529:28: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
INTEGER(tlen)[j] = header->target_len[j];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:594:49: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
bam_seek(bd->bfile->file->x.bam, bd->bfile->pos0, SEEK_SET);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:61:46: note: expanded from macro 'bam_seek'
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^
io_sam.c:628:31: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
bd->bfile->pos0 = bam_tell(bd->bfile->file->x.bam);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:638:27: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
bd->bfile->pos0 = bam_tell(bd->bfile->file->x.bam);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:748:50: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
bd->CIGAR_BUF, bd->CIGAR_BUF_SZ) < 0) {
˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:809:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
INTEGER(width)[i] = strlen(key[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
io_sam.c:819:57: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
dest.length, seq, strlen(seq), lkup0,
^˜˜˜˜˜˜˜˜˜˜
io_sam.c:891:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->flag, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:891:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->flag, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:897:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->rname, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:897:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->rname, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:905:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->strand, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:905:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->strand, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:914:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->pos, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:914:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->pos, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:920:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->qwidth, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:920:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->qwidth, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:926:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->mapq, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:926:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->mapq, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:932:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->mrnm, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:932:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->mrnm, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:940:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->mpos, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:940:48: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->mpos, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:946:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->isize, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
io_sam.c:946:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(INTEGER(s), sbd->isize, sbd->icnt * sizeof(int));
˜˜˜˜˜^˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
io_sam.c:1052:76: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
INTEGER(VECTOR_ELT(result, 0))[i] = REAL(VECTOR_ELT(result, 1))[i] = 0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
54 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c pileupbam.c -o pileupbam.o
In file included from pileupbam.c:1:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from pileupbam.c:2:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
pileupbam.c:271:44: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(opos), 0, sizeof(int) * Rf_length(opos));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
pileupbam.c:271:44: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(opos), 0, sizeof(int) * Rf_length(opos));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
pileupbam.c:278:48: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(oseq), 0, sizeof(int) * Rf_length(oseq));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
pileupbam.c:278:48: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(oseq), 0, sizeof(int) * Rf_length(oseq));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
pileupbam.c:302:49: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(oqual), 0, sizeof(int) * Rf_length(oqual));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
pileupbam.c:302:49: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(oqual), 0, sizeof(int) * Rf_length(oqual));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
pileupbam.c:580:34: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memset(cnt, 0, sizeof(int) * n_spc);
˜ ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
pileupbam.c:580:34: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memset(cnt, 0, sizeof(int) * n_spc);
˜ ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
pileupbam.c:675:22: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
p.keep_flag[0] = INTEGER(_lst_elt(param, "flag", "param"))[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pileupbam.c:676:22: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
p.keep_flag[1] = INTEGER(_lst_elt(param, "flag", "param"))[1];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools_patch.c -o samtools_patch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tabixfile.c -o tabixfile.o
In file included from tabixfile.c:1:
In file included from ./tabixfile.h:5:
In file included from ./tabix/tabix.h:32:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
tabixfile.c:143:16: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
curr_off = bgzf_tell(tabix->fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabixfile.c:147:13: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
curr_off = bgzf_tell(tabix->fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabixfile.c:155:26: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
bgzf_seek(tabix->fp, curr_off, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
tabixfile.c:246:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
nrec = nrec * SCALE;
˜ ˜˜˜˜˜^˜˜˜˜˜˜
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c utilities.c -o utilities.o
utilities.c:106:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int i = strlen(s) - 1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zip_compression.c -o zip_compression.o
zip_compression.c:9:5: warning: implicit declaration of function 'close' is invalid in C99 [-Wimplicit-function-declaration]
close(infd);
^
zip_compression.c:64:23: warning: implicit declaration of function 'read' is invalid in C99 [-Wimplicit-function-declaration]
while (0 < (cnt = read(infd, buffer, BUF_SIZE)))
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c:88:14: warning: implicit conversion loses integer precision: 'uint16_t' (aka 'unsigned short') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
buffer[0] = value;
˜ ^˜˜˜˜
samtools/bgzf.c:99:14: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
buffer[0] = value;
˜ ^˜˜˜˜
samtools/bgzf.c:100:20: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
buffer[1] = value >> 8;
˜ ˜˜˜˜˜˜^˜˜˜
samtools/bgzf.c:101:20: warning: implicit conversion loses integer precision: 'uint32_t' (aka 'unsigned int') to 'uint8_t' (aka 'unsigned char') [-Wconversion]
buffer[2] = value >> 16;
˜ ˜˜˜˜˜˜^˜˜˜˜
samtools/bgzf.c:204:16: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
zs.avail_in = slen;
˜ ^˜˜˜
samtools/bgzf.c:206:45: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:213:28: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bgzf.c:215:40: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
crc = crc32(crc32(0L, NULL, 0L), src, slen);
˜˜˜˜˜ ^˜˜˜
samtools/bgzf.c:217:39: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
packInt32((uint8_t*)&dst[*dlen - 4], slen);
˜˜˜˜˜˜˜˜˜ ^˜˜˜
samtools/bgzf.c:210:45: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
*dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:215:8: warning: implicit conversion loses integer precision: 'uLong' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
crc = crc32(crc32(0L, NULL, 0L), src, slen);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:239:36: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
zs.next_in = fp->compressed_block + 18;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
samtools/bgzf.c:240:29: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
zs.avail_in = block_length - 16;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/bgzf.c:257:12: warning: implicit conversion loses integer precision: 'uLong' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return zs.total_out;
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
samtools/bgzf.c:334:10: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
count = _bgzf_read(fp->fp, header, sizeof(header));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:44:34: note: expanded from macro '_bgzf_read'
#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:348:10: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:44:34: note: expanded from macro '_bgzf_read'
#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:376:57: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
copy_length = length - bytes_read < available? length - bytes_read : available;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:448:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mt->len = calloc(mt->n_blks, sizeof(int));
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
samtools/bgzf.c:449:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mt->blk = calloc(mt->n_blks, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
samtools/bgzf.c:452:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mt->tid = calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/bgzf.c:453:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mt->w = calloc(mt->n_threads, sizeof(worker_t));
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/bgzf.c:516:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (fwrite(mt->blk[i], 1, mt->len[i], fp->fp) != mt->len[i])
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:537:33: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/usr/include/secure/_string.h:51:21: note: expanded from macro 'memcpy'
((__darwin_obsz0 (dest) != (size_t) -1) \
^
/usr/include/secure/_common.h:38:55: note: expanded from macro '__darwin_obsz0'
#define __darwin_obsz0(object) __builtin_object_size (object, 0)
^
samtools/bgzf.c:537:33: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/usr/include/secure/_string.h:52:30: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
samtools/bgzf.c:537:33: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/usr/include/secure/_string.h:52:62: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
/usr/include/secure/_common.h:38:55: note: expanded from macro '__darwin_obsz0'
#define __darwin_obsz0(object) __builtin_object_size (object, 0)
^
samtools/bgzf.c:537:33: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/usr/include/secure/_string.h:53:27: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
samtools/bgzf.c:536:101: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
int copy_length = BGZF_BLOCK_SIZE - fp->block_offset < rest? BGZF_BLOCK_SIZE - fp->block_offset : rest;
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
samtools/bgzf.c:554:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) {
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:580:120: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written;
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:598:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
count = fwrite(fp->compressed_block, 1, block_length, fp->fp);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:598:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
count = fwrite(fp->compressed_block, 1, block_length, fp->fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:658:6: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
n = _bgzf_read(fp, buf, 16);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:44:34: note: expanded from macro '_bgzf_read'
#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bgzf.c:697:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (str->l + l + 1 >= str->m) {
˜ ^
samtools/bgzf.c:698:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
str->m = str->l + l + 2;
˜ ^
samtools/bgzf.c:703:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
str->l += l;
˜˜ ^
samtools/bgzf.c:713:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return str->l;
˜˜˜˜˜˜ ˜˜˜˜˜^
36 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/kstring.c -o samtools/kstring.o
In file included from samtools/kstring.c:6:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
samtools/kstring.c:16:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
samtools/kstring.c:23:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
samtools/kstring.c:74:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (isgraph(last_char)) __ksplit_aux; // the end of a field
^˜˜˜˜˜˜˜˜˜˜˜
samtools/kstring.c:65:52: note: expanded from macro '__ksplit_aux'
offsets = (int*)realloc(offsets, sizeof(int) * max); \
˜ ^˜˜
samtools/kstring.c:80:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
^˜˜˜˜˜˜˜˜˜˜˜
samtools/kstring.c:65:52: note: expanded from macro '__ksplit_aux'
offsets = (int*)realloc(offsets, sizeof(int) * max); \
˜ ^˜˜
samtools/kstring.c:58:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
l = strlen(s);
˜ ^˜˜˜˜˜˜˜˜
samtools/kstring.c:101:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
prep = (int*)calloc(m + 256, sizeof(int));
˜˜˜˜˜˜ ˜˜^˜˜˜˜
samtools/kstring.c:107:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
suff = (int*)calloc(m, sizeof(int));
˜˜˜˜˜˜ ^
samtools/kstring.c:161:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/kstring.c:161:47: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/kstring.c:166:37: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
21 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_aux.c -o samtools/bam_aux.o
In file included from samtools/bam_aux.c:2:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from samtools/bam_aux.c:3:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools/bam_aux.c:16:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)realloc(b->data, b->m_data);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_aux.c:18:21: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
˜ ^˜˜˜˜˜
samtools/bam_aux.c:18:52: warning: implicit conversion changes signedness: 'const char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
˜ ^˜˜˜˜˜
samtools/bam_aux.c:19:25: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
b->data[ori_len + 2] = type;
˜ ^˜˜˜
samtools/bam_aux.c:71:16: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
b->l_aux = s - p;
˜ ˜˜^˜˜
samtools/bam_aux.c:119:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = (char*)malloc(l+1);
˜˜˜˜˜˜ ˜^˜
samtools/bam_aux.c:118:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
name_end = l = strlen(str);
˜ ^˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam.c -o samtools/bam.o
In file included from samtools/bam.c:5:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from samtools/bam.c:7:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
samtools/bam.c:40:9: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
return end;
˜˜˜˜˜˜ ^˜˜
samtools/bam.c:110:47: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/bam.c:111:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
header->target_len = (uint32_t*)calloc(header->n_targets, 4);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/bam.c:115:42: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
header->target_name[i] = (char*)calloc(name_len, 1);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
samtools/bam.c:96:14: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
magic_len = bam_read(fp, buf, 4);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:58:33: note: expanded from macro 'bam_read'
#define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:132:7: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
x = bam_swap_endian_4(header->l_text);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:135:7: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
x = bam_swap_endian_4(header->n_targets);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:135:33: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x = bam_swap_endian_4(header->n_targets);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/bam.c:147:8: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
x = bam_swap_endian_4(name_len);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:147:26: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x = bam_swap_endian_4(name_len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
samtools/bam.c:152:8: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
x = bam_swap_endian_4(header->target_len[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:145:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
name_len = strlen(p) + 1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam.c:169:10: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
type = toupper(*s); ++s; // skip type
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:207:11: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
c->tid = x[0]; c->pos = x[1];
˜ ^˜˜˜
samtools/bam.c:207:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
c->tid = x[0]; c->pos = x[1];
˜ ^˜˜˜
samtools/bam.c:210:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
c->l_qseq = x[4];
˜ ^˜˜˜
samtools/bam.c:211:12: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
˜ ^˜˜˜
samtools/bam.c:211:28: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
˜ ^˜˜˜
samtools/bam.c:211:45: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
˜ ^˜˜˜
samtools/bam.c:212:26: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
b->data_len = block_len - BAM_CORE_SIZE;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:212:16: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
b->data_len = block_len - BAM_CORE_SIZE;
^˜˜˜˜˜˜˜˜ ˜
samtools/bam.c:216:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)realloc(b->data, b->m_data);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam.c:198:13: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
if ((ret = bam_read(fp, &block_len, 4)) != 4) {
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:58:33: note: expanded from macro 'bam_read'
#define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:227:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
^˜˜˜˜˜˜˜ ˜
samtools/bam.c:230:12: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x[0] = c->tid;
˜ ˜˜˜^˜˜
samtools/bam.c:231:12: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x[1] = c->pos;
˜ ˜˜˜^˜˜
samtools/bam.c:232:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
˜ ˜˜˜˜˜˜˜^˜˜
samtools/bam.c:234:12: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x[4] = c->l_qseq;
˜ ˜˜˜^˜˜˜˜˜
samtools/bam.c:235:12: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x[5] = c->mtid;
˜ ˜˜˜^˜˜˜
samtools/bam.c:236:12: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x[6] = c->mpos;
˜ ˜˜˜^˜˜˜
samtools/bam.c:237:12: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
x[7] = c->isize;
˜ ˜˜˜^˜˜˜˜
samtools/bam.c:240:27: warning: static function 'bam_swap_endian_4p' is used in an inline function with external linkage [-Wstatic-in-inline]
for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
^
./samtools/bam.h:453:2: note: use 'static' to give inline function 'bam_write1_core' internal linkage
int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
^
static
./samtools/bam_endian.h:25:21: note: 'bam_swap_endian_4p' declared here
static inline void *bam_swap_endian_4p(void *x)
^
samtools/bam.c:242:17: warning: static function 'bam_swap_endian_4p' is used in an inline function with external linkage [-Wstatic-in-inline]
bam_write(fp, bam_swap_endian_4p(&y), 4);
^
./samtools/bam.h:59:49: note: expanded from macro 'bam_write'
#define bam_write(fp, buf, size) bgzf_write(fp, buf, size)
^
./samtools/bam.h:453:2: note: use 'static' to give inline function 'bam_write1_core' internal linkage
int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
^
static
./samtools/bam_endian.h:25:21: note: 'bam_swap_endian_4p' declared here
static inline void *bam_swap_endian_4p(void *x)
^
samtools/bam.c:243:3: warning: static function 'swap_endian_data' is used in an inline function with external linkage [-Wstatic-in-inline]
swap_endian_data(c, data_len, data);
^
./samtools/bam.h:453:2: note: use 'static' to give inline function 'bam_write1_core' internal linkage
int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
^
static
samtools/bam.c:160:13: note: 'swap_endian_data' declared here
static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
^
samtools/bam.c:247:17: warning: static function 'swap_endian_data' is used in an inline function with external linkage [-Wstatic-in-inline]
if (bam_is_be) swap_endian_data(c, data_len, data);
^
./samtools/bam.h:453:2: note: use 'static' to give inline function 'bam_write1_core' internal linkage
int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);
^
static
samtools/bam.c:160:13: note: 'swap_endian_data' declared here
static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
^
samtools/bam.c:248:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return 4 + block_len;
˜˜˜˜˜˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:398:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)realloc(b->data, b->m_data);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam.c:418:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:437:10: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
bam1_seq_seti(seq, j+u, c);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:262:82: note: expanded from macro 'bam1_seq_seti'
#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((˜(i)&1)<<2) )
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:442:8: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
bam1_seq_seti(seq, j+u, c);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:262:82: note: expanded from macro 'bam1_seq_seti'
#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((˜(i)&1)<<2) )
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam.c:467:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
˜ ^
samtools/bam.c:468:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
b->data_len = p - b->data; // update record length
˜ ˜˜^˜˜˜˜˜˜˜˜
55 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_import.c -o samtools/bam_import.o
In file included from samtools/bam_import.c:13:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
In file included from samtools/bam_import.c:14:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from samtools/bam_import.c:17:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools/bam_import.c:19:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(gzFile, gzread, 16384)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:121:26: note: expanded from macro '__KS_GETUNTIL'
str->m = str->l + (i - ks->begin) + 1; \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:19:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(gzFile, gzread, 16384)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:126:25: note: expanded from macro '__KS_GETUNTIL'
str->l = str->l + (i - ks->begin); \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:19:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSTREAM_INIT(gzFile, gzread, 16384)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:138:15: note: expanded from macro '__KS_GETUNTIL'
return str->l; \
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bam_import.c:86:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
list = (char**)realloc(list, m * sizeof(char*));
^ ˜
samtools/bam_import.c:105:22: warning: implicit conversion changes signedness: 'const khint_t' (aka 'const unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
header->n_targets = kh_size(hash);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/khash.h:471:26: note: expanded from macro 'kh_size'
#define kh_size(h) ((h)->size)
˜˜˜˜˜^˜˜˜
samtools/bam_import.c:136:7: warning: implicit conversion changes signedness: 'khint_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
i = kh_size(hash);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/khash.h:471:26: note: expanded from macro 'kh_size'
#define kh_size(h) ((h)->size)
˜˜˜˜˜^˜˜˜
samtools/bam_import.c:144:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
kh_value(hash, k) = (uint64_t)len<<32 | i;
˜ ^
samtools/bam_import.c:162:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)realloc(b->data, b->m_data);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_import.c:177:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
header->n_text = y;
˜ ^
samtools/bam_import.c:206:29: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->target_name = calloc(h->n_targets, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
samtools/bam_import.c:211:28: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->target_len = calloc(h->n_targets, 4);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
samtools/bam_import.c:213:22: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
h->target_len[i] = atoi(tmp[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:224:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
str->s[str->l] = dret; // note that str->s is NOT null terminated!!
˜ ^˜˜˜
samtools/bam_import.c:285:97: warning: operand of ? changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:299:44: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:316:26: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
else parse_error(fp->n_lines, "invalid CIGAR operation");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:320:28: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:321:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:321:28: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^˜˜
samtools/bam_import.c:328:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
c->bin = bam_reg2bin(c->pos, c->pos + 1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:328:28: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
c->bin = bam_reg2bin(c->pos, c->pos + 1);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^˜˜
samtools/bam_import.c:328:40: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
c->bin = bam_reg2bin(c->pos, c->pos + 1);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
samtools/bam_import.c:350:21: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:360:20: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
parse_error(fp->n_lines, "sequence and quality are inconsistent");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:363:57: warning: implicit conversion changes signedness: 'int' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/bam_import.c:372:21: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
parse_error(fp->n_lines, "missing colon in auxiliary data");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:373:13: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
key[0] = str->s[0]; key[1] = str->s[1];
˜ ^˜˜˜˜˜˜˜˜
samtools/bam_import.c:373:33: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
key[0] = str->s[0]; key[1] = str->s[1];
˜ ^˜˜˜˜˜˜˜˜
samtools/bam_import.c:374:11: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
type = str->s[3];
˜ ^˜˜˜˜˜˜˜˜
samtools/bam_import.c:379:22: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
*s++ = 'A'; *s = str->s[5];
˜ ^˜˜˜˜˜˜˜˜
samtools/bam_import.c:428:49: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:432:24: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
parse_error(fp->n_lines, "invalid hex character");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:443:37: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:450:24: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
*s++ = 'B'; *s++ = str->s[5];
˜ ^˜˜˜˜˜˜˜˜
samtools/bam_import.c:459:26: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
else parse_error(fp->n_lines, "unrecognized array type");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:461:27: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
} else parse_error(fp->n_lines, "unrecognized type");
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bam_import.c:248:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
ret = str->l;
˜ ˜˜˜˜˜^
samtools/bam_import.c:260:31: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
c->l_qname = strlen(str->s) + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_import.c:274:13: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
c->flag = flag;
˜ ^˜˜˜
samtools/bam_import.c:318:16: warning: implicit conversion loses integer precision: 'long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
cigar[i] = bam_cigar_gen(x, op);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:164:50: note: expanded from macro 'bam_cigar_gen'
#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/bam_import.c:346:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
c->l_qseq = strlen(str->s);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_import.c:425:33: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int size = 1 + (str->l - 5) + 1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
57 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/sam.c -o samtools/sam.o
In file included from samtools/sam.c:6:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
samtools/sam.c:20:39: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->target_len = (uint32_t*)calloc(h->n_targets, 4);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
samtools/sam.c:21:37: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜
samtools/sam.c:30:25: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int x = header->l_text + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/sam.c:31:31: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int y = header->l_text + len + 1; // 1 byte null
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/sam.c:31:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int y = header->l_text + len + 1; // 1 byte null
˜ ^˜˜
samtools/sam.c:35:57: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (x < y) header->text = (char*)realloc(header->text, y);
˜˜˜˜˜˜˜ ^
samtools/sam.c:37:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
header->l_text += len;
˜˜ ^˜˜
samtools/sam.c:68:67: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
append_header_text(fp->header, textheader->text, textheader->l_text);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
samtools/sam.c:83:70: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
samtools/sam.c:147:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int l = strlen(s);
˜ ^˜˜˜˜˜˜˜˜
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_index.c -o samtools/bam_index.o
In file included from samtools/bam_index.c:3:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from samtools/bam_index.c:4:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools/bam_index.c:52:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSORT_INIT(off, pair64_t, pair64_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:201:81: note: expanded from macro 'KSORT_INIT'
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
˜^
samtools/bam_index.c:52:1: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
KSORT_INIT(off, pair64_t, pair64_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:206:31: note: expanded from macro 'KSORT_INIT'
ks_combsort_##name(t - s + 1, s); \
˜˜˜˜˜˜^˜˜
samtools/bam_index.c:52:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(off, pair64_t, pair64_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:271:12: note: expanded from macro 'KSORT_INIT'
for (i = n; i > 1; --i) { \
˜ ^
samtools/bam_index.c:79:19: warning: implicit conversion changes signedness: 'int' to 'khint32_t' (aka 'unsigned int') [-Wsign-conversion]
k = kh_put(i, h, bin, &ret);
˜˜˜˜˜˜˜˜ ^˜˜
./samtools/khash.h:402:48: note: expanded from macro 'kh_put'
#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
^
samtools/bam_index.c:101:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_index.c:134:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
p->n = m + 1;
˜ ˜˜^˜˜
samtools/bam_index.c:174:41: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bam_index.c:176:41: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bam_index.c:178:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:178:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:179:24: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:179:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:181:22: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
off_beg = off_end = bam_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:199:41: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
samtools/bam_index.c:219:14: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
last_off = bam_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:223:39: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
samtools/bam_index.c:223:59: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:224:61: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:269:21: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t x = idx->n;
˜ ˜˜˜˜˜^
samtools/bam_index.c:276:10: warning: implicit conversion changes signedness: 'khint_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
size = kh_size(index);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/khash.h:471:26: note: expanded from macro 'kh_size'
#define kh_size(h) ((h)->size)
˜˜˜˜˜^˜˜˜
samtools/bam_index.c:278:17: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t x = size;
˜ ^˜˜˜
samtools/bam_index.c:313:38: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(index2->offset, 8, index2->n, fp);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
samtools/bam_index.c:316:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
} else fwrite(index2->offset, 8, index2->n, fp);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
samtools/bam_index.c:344:41: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bam_index.c:345:41: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bam_index.c:379:46: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index2->offset = (uint64_t*)calloc(index2->m, 8);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
samtools/bam_index.c:380:33: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fread(index2->offset, index2->n, 8, fp);
˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
samtools/bam_index.c:396:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int l = strlen(_fn);
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:446:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(buf, 1, l, fp);
˜˜˜˜˜˜ ^
samtools/bam_index.c:430:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
l = strlen(url);
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:445:14: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:565:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
˜ ^
samtools/bam_index.c:566:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
˜ ^
samtools/bam_index.c:567:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
˜ ^
samtools/bam_index.c:568:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
˜ ^
samtools/bam_index.c:569:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
˜ ^
samtools/bam_index.c:575:26: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t rbeg = b->core.pos;
˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜
samtools/bam_index.c:576:85: warning: operand of ? changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_index.c:605:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
n_bins = reg2bins(beg, end, bins);
˜˜˜˜˜˜˜˜ ^˜˜
samtools/bam_index.c:605:25: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
n_bins = reg2bins(beg, end, bins);
˜˜˜˜˜˜˜˜ ^˜˜
samtools/bam_index.c:625:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
off = (pair64_t*)calloc(n_off, 16);
˜˜˜˜˜˜ ^˜˜˜˜
samtools/bam_index.c:641:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ks_introsort(off, n_off, off);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./samtools/ksort.h:279:54: note: expanded from macro 'ks_introsort'
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
^
samtools/bam_index.c:699:39: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:61:46: note: expanded from macro 'bam_seek'
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^
samtools/bam_index.c:700:22: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
iter->curr_off = bam_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:705:21: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
iter->curr_off = bam_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/bam.h:60:22: note: expanded from macro 'bam_tell'
#define bam_tell(fp) bgzf_tell(fp)
^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_index.c:710:30: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
else if (is_overlap(iter->beg, iter->end, b)) return ret;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bam_index.c:710:41: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
else if (is_overlap(iter->beg, iter->end, b)) return ret;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
51 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_pileup.c -o samtools/bam_pileup.o
In file included from samtools/bam_pileup.c:5:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
samtools/bam_pileup.c:54:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
˜ ˜˜˜˜^˜˜
samtools/bam_pileup.c:94:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (pos - s->x >= l) { // jump to the next operation
˜ ˜˜˜^
samtools/bam_pileup.c:134:19: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
p->qpos = s->y + (pos - s->x);
˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_pileup.c:134:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
p->qpos = s->y + (pos - s->x);
˜˜˜^ ˜
samtools/bam_pileup.c:134:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
p->qpos = s->y + (pos - s->x);
˜ ˜˜˜^
samtools/bam_pileup.c:209:83: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜
samtools/bam_pileup.c:212:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bam_pileup.c:227:64: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_pileup.c:229:28: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
iter->pos = iter->head->beg; // jump to the next position
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_pileup.c:246:29: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
˜ ˜˜˜˜˜˜˜˜^˜˜
samtools/bam_pileup.c:247:70: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_pileup.c:258:60: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_pileup.c:366:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
buf->func(tid, pos, n_plp, plp, buf->data);
˜˜˜ ^˜˜
samtools/bam_pileup.c:366:18: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
buf->func(tid, pos, n_plp, plp, buf->data);
˜˜˜ ^˜˜
samtools/bam_pileup.c:387:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
iter->pos = calloc(n, 8);
˜˜˜˜˜˜ ^
samtools/bam_pileup.c:388:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
iter->n_plp = calloc(n, sizeof(int));
˜˜˜˜˜˜ ^
samtools/bam_pileup.c:389:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
iter->plp = calloc(n, sizeof(void*));
˜˜˜˜˜˜ ^
samtools/bam_pileup.c:390:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
iter->iter = calloc(n, sizeof(void*));
˜˜˜˜˜˜ ^
samtools/bam_pileup.c:423:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
iter->pos[i] = (uint64_t)tid<<32 | pos;
˜ ^˜˜
samtools/bam_pileup.c:429:17: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wsign-conversion]
*_tid = new_min>>32; *_pos = (uint32_t)new_min;
˜ ˜˜˜˜˜˜˜^˜˜˜
samtools/bam_pileup.c:429:31: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
*_tid = new_min>>32; *_pos = (uint32_t)new_min;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
23 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
In file included from samtools/bam_lpileup.c:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
samtools/bam_lpileup.c:15:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSORT_INIT(node, freenode_p, freenode_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:201:81: note: expanded from macro 'KSORT_INIT'
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
˜^
samtools/bam_lpileup.c:15:1: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
KSORT_INIT(node, freenode_p, freenode_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:206:31: note: expanded from macro 'KSORT_INIT'
ks_combsort_##name(t - s + 1, s); \
˜˜˜˜˜˜^˜˜
samtools/bam_lpileup.c:15:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(node, freenode_p, freenode_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:271:12: note: expanded from macro 'KSORT_INIT'
for (i = n; i > 1; --i) { \
˜ ^
samtools/bam_lpileup.c:44:70: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
˜ ˜˜˜˜^˜˜
samtools/bam_lpileup.c:85:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
˜ ˜˜˜˜^˜˜
samtools/bam_lpileup.c:86:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
˜ ˜˜˜˜^˜˜
samtools/bam_lpileup.c:107:23: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
tv->tail->level = tv->cur_level[i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_lpileup.c:124:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tv->aux = (freenode_t**)realloc(tv->aux, sizeof(void*) * tv->m_aux);
˜ ˜˜˜˜^˜˜˜˜
samtools/bam_lpileup.c:139:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ks_introsort(node, tv->n_nodes, tv->aux);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
./samtools/ksort.h:279:54: note: expanded from macro 'ks_introsort'
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_md.c -o samtools/bam_md.o
In file included from samtools/bam_md.c:7:
In file included from ./samtools/sam.h:4:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
In file included from samtools/bam_md.c:8:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
samtools/bam_md.c:103:52: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
samtools/bam_md.c:115:41: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
samtools/bam_md.c:213:49: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64);
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_md.c:248:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
bq = calloc(c->l_qseq + 1, 1);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_md.c:250:17: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = calloc(c->l_qseq, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_md.c:251:42: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_md.c:252:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
r = calloc(xe - xb, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜
samtools/bam_md.c:255:14: warning: implicit conversion changes signedness: 'char' to 'uint8_t' (aka 'unsigned char') [-Wsign-conversion]
r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_md.c:257:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
state = calloc(c->l_qseq, sizeof(int));
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_md.c:258:17: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
q = calloc(c->l_qseq, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_md.c:275:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_md.c:275:50: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
25 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/razf.c -o samtools/razf.o
samtools/razf.c:83:41: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rz->index->cap = rz->index->cap * 1.5 + 2;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/razf.c:84:87: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/razf.c:85:91: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
rz->index->bin_offsets = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/razf.c:87:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
samtools/razf.c:87:75: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
samtools/razf.c:88:85: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
samtools/razf.c:88:49: warning: implicit conversion loses integer precision: 'long long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:98:9: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
v32 = byte_swap_4((uint32_t)rz->index->size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:101:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
v32 = rz->index->size / RZ_BIN_SIZE + 1;
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
samtools/razf.c:103:51: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:106:54: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
˜ ^˜˜
samtools/razf.c:107:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/razf.c:126:31: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:128:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
v32 = rz->index->size / RZ_BIN_SIZE + 1;
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜ ˜
samtools/razf.c:129:53: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
rz->index->bin_offsets = malloc(sizeof(int64_t) * v32);
˜ ^˜˜
samtools/razf.c:131:58: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
˜ ^˜˜
samtools/razf.c:135:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/razf.c:137:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
samtools/razf.c:142:50: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:193:25: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
rz->stream->avail_in = size;
˜ ^˜˜˜
samtools/razf.c:196:22: warning: implicit conversion changes signedness: 'uInt' (aka 'unsigned int') to 'int' [-Wsign-conversion]
tout = rz->stream->avail_out;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/razf.c:198:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
rz->out += tout - rz->stream->avail_out;
^˜˜˜ ˜
samtools/razf.c:209:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
rz->in += size - rz->stream->avail_in;
^˜˜˜ ˜
samtools/razf.c:210:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
rz->block_off += size - rz->stream->avail_in;
^˜˜˜ ˜
samtools/razf.c:283:9: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
data += n;
˜˜˜˜ ^
samtools/razf.c:297:8: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
data += n;
˜˜˜˜ ^
samtools/razf.c:295:27: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
n = next_block - rz->in - rz->buf_len;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:391:27: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
rz->stream->avail_in = n - rz->header_size;
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:392:35: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
rz->stream->next_in = rz->inbuf + rz->header_size;
˜˜˜˜˜˜˜˜˜ ^
samtools/razf.c:400:37: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz;
˜˜˜˜˜˜˜˜˜ ^
samtools/razf.c:373:9: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:436:12: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
n = rz->end;
˜ ˜˜˜˜^˜˜
samtools/razf.c:511:9: warning: ordered comparison between pointer and zero ('knetFile *' (aka 'struct knetFile_s *') and 'int') is an extension [-Wpedantic]
if(fd < 0) return NULL;
˜˜ ^ ˜
samtools/razf.c:577:26: warning: implicit conversion changes signedness: 'int' to 'uInt' (aka 'unsigned int') [-Wsign-conversion]
rz->stream->avail_out = size;
˜ ^˜˜˜
samtools/razf.c:601:21: warning: implicit conversion changes signedness: 'uInt' (aka 'unsigned int') to 'int' [-Wsign-conversion]
tin = rz->stream->avail_in;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
samtools/razf.c:603:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
rz->in += tin - rz->stream->avail_in;
^˜˜ ˜
samtools/razf.c:619:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return size - rz->stream->avail_out;
˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:619:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return size - rz->stream->avail_out;
^˜˜˜ ˜
samtools/razf.c:570:9: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
ret = knet_read(rz->x.fpr, data, size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:584:28: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:590:28: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'uInt' (aka 'unsigned int') [-Wshorten-64-to-32]
rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/razf.c:631:10: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
data += size;
˜˜˜˜ ^
samtools/razf.c:637:10: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
data += rz->buf_len;
˜˜˜˜ ^
samtools/razf.c:770:95: warning: implicit conversion changes signedness: 'int64_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
^˜˜ ˜
44 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/faidx.c -o samtools/faidx.o
In file included from samtools/faidx.c:7:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools/faidx.c:55:63: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
idx->name = (char**)realloc(idx->name, sizeof(void*) * idx->m);
˜ ˜˜˜˜˜^
samtools/faidx.c:81:14: warning: implicit conversion changes signedness: 'int64_t' (aka 'long long') to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
offset = razf_tell(rz);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/razf.h:123:30: note: expanded from macro 'razf_tell'
#define razf_tell(rz) ((rz)->out)
˜˜˜˜˜˜^˜˜
samtools/faidx.c:93:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
name = (char*)realloc(name, m_name);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
samtools/faidx.c:100:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
name = (char*)realloc(name, m_name);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
samtools/faidx.c:110:13: warning: implicit conversion changes signedness: 'int64_t' (aka 'long long') to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
offset = razf_tell(rz);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/razf.h:123:30: note: expanded from macro 'razf_tell'
#define razf_tell(rz) ((rz)->out)
˜˜˜˜˜˜^˜˜
samtools/faidx.c:87:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
fai_insert_index(idx, name, len, line_len, line_blen, offset);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
samtools/faidx.c:140:33: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
fai_insert_index(idx, name, len, line_len, line_blen, offset);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
samtools/faidx.c:182:56: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
fai_insert_index(fai, buf, len, line_len, line_blen, offset);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
samtools/faidx.c:263:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(buf, 1, l, fp);
˜˜˜˜˜˜ ^
samtools/faidx.c:240:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int l = strlen(fn);
˜ ^˜˜˜˜˜˜˜˜˜
samtools/faidx.c:262:17: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:329:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = (char*)malloc(l+1);
˜˜˜˜˜˜ ˜^˜
samtools/faidx.c:377:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = (char*)malloc(end - beg + 2);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/faidx.c:378:69: warning: implicit conversion changes signedness: 'unsigned long long' to 'int64_t' (aka 'long long') [-Wsign-conversion]
razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:378:54: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:378:75: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:328:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
name_end = l = strlen(str);
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:367:38: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
end = i < k? atoi(s + i + 1) : val.len;
˜ ˜˜˜˜^˜˜
samtools/faidx.c:369:28: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
} else beg = 0, end = val.len;
˜ ˜˜˜˜^˜˜
samtools/faidx.c:370:32: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
if (beg >= val.len) beg = val.len;
˜ ˜˜˜˜^˜˜
samtools/faidx.c:371:32: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
if (end >= val.len) end = val.len;
˜ ˜˜˜˜^˜˜
samtools/faidx.c:442:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
seq = (char*)malloc(p_end_i - p_beg_i + 2);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/faidx.c:443:73: warning: implicit conversion changes signedness: 'unsigned long long' to 'int64_t' (aka 'long long') [-Wsign-conversion]
razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:443:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:443:83: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/faidx.c:436:51: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
˜ ˜˜˜˜˜˜˜˜^˜˜
samtools/faidx.c:438:51: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
else if(val.len <= p_end_i) p_end_i = val.len - 1;
˜ ˜˜˜˜˜˜˜˜^˜˜
29 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c:192:26: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
curr = netread(fd, buf + l, rest);
˜˜˜ ^
./samtools/knetfile.h:8:40: note: expanded from macro 'netread'
#define netread(fd, ptr, len) read(fd, ptr, len)
^
samtools/knetfile.c:192:31: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
curr = netread(fd, buf + l, rest);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./samtools/knetfile.h:8:45: note: expanded from macro 'netread'
#define netread(fd, ptr, len) read(fd, ptr, len)
^
samtools/knetfile.c:221:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ftp->response = realloc(ftp->response, ftp->max_response);
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
samtools/knetfile.c:223:24: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
ftp->response[n++] = c;
˜ ^
samtools/knetfile.c:233:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return strtol(ftp->response, &p, 0);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/knetfile.c:310:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fp->host = calloc(l + 1, 1);
˜˜˜˜˜˜ ˜˜^˜˜
samtools/knetfile.c:303:13: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
l = p - fn - 6;
˜ ˜˜˜˜˜˜˜^˜˜
samtools/knetfile.c:383:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fp->http_host = calloc(l + 1, 1);
˜˜˜˜˜˜ ˜˜^˜˜
samtools/knetfile.c:381:13: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
l = p - fn - 7;
˜ ˜˜˜˜˜˜˜^˜˜
samtools/knetfile.c:418:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
netwrite(fp->fd, buf, l);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./samtools/knetfile.h:9:47: note: expanded from macro 'netwrite'
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
samtools/knetfile.c:431:8: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
ret = strtol(buf + 8, &p, 0); // HTTP return code
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/knetfile.c:523:29: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
curr = read(fp->fd, buf + l, rest);
˜˜˜ ^
samtools/knetfile.c:523:34: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
curr = read(fp->fd, buf + l, rest);
˜˜˜˜ ^˜˜˜
13 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_sort.c -o samtools/bam_sort.o
In file included from samtools/bam_sort.c:10:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
samtools/bam_sort.c:59:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSORT_INIT(heap, heap1_t, heap_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:201:81: note: expanded from macro 'KSORT_INIT'
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
˜^
samtools/bam_sort.c:59:1: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
KSORT_INIT(heap, heap1_t, heap_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:206:31: note: expanded from macro 'KSORT_INIT'
ks_combsort_##name(t - s + 1, s); \
˜˜˜˜˜˜^˜˜
samtools/bam_sort.c:59:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(heap, heap1_t, heap_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:271:12: note: expanded from macro 'KSORT_INIT'
for (i = n; i > 1; --i) { \
˜ ^
samtools/bam_sort.c:73:14: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
˜ ˜˜˜˜^˜˜˜˜˜
samtools/bam_sort.c:73:60: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
˜ ^˜˜˜˜
samtools/bam_sort.c:117:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fp = (bamFile*)calloc(n, sizeof(bamFile));
˜˜˜˜˜˜ ^
samtools/bam_sort.c:118:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
˜˜˜˜˜˜ ^
samtools/bam_sort.c:119:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
˜˜˜˜˜˜ ^
samtools/bam_sort.c:122:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
RG = (char**)calloc(n, sizeof(void*));
˜˜˜˜˜˜ ^
samtools/bam_sort.c:123:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
RG_len = (int*)calloc(n, sizeof(int));
˜˜˜˜˜˜ ^
samtools/bam_sort.c:130:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
RG[i] = calloc(l + 1, 1);
˜˜˜˜˜˜ ˜˜^˜˜
samtools/bam_sort.c:229:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ks_heapmake(heap, n, heap);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./samtools/ksort.h:282:52: note: expanded from macro 'ks_heapmake'
#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
^
samtools/bam_sort.c:246:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ks_heapadjust(heap, 0, n, heap);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
./samtools/ksort.h:283:62: note: expanded from macro 'ks_heapadjust'
#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
^
samtools/bam_sort.c:125:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int l = strlen(fn[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_sort.c:336:34: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (strncmp(q + 4, so, p - q - 4) != 0) {
˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bam_sort.c:350:20: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
samtools/bam_sort.c:350:73: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
samtools/bam_sort.c:350:50: warning: implicit conversion loses integer precision: 'unsigned long' to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bam_sort.c:366:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_sort.c:366:123: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_sort.c:368:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSORT_INIT(sort, bam1_p, bam1_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:201:81: note: expanded from macro 'KSORT_INIT'
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
˜^
samtools/bam_sort.c:368:1: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
KSORT_INIT(sort, bam1_p, bam1_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:206:31: note: expanded from macro 'KSORT_INIT'
ks_combsort_##name(t - s + 1, s); \
˜˜˜˜˜˜^˜˜
samtools/bam_sort.c:368:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(sort, bam1_p, bam1_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:271:12: note: expanded from macro 'KSORT_INIT'
for (i = n; i > 1; --i) { \
˜ ^
samtools/bam_sort.c:416:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
w = calloc(n_threads, sizeof(worker_t));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
samtools/bam_sort.c:417:15: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tid = calloc(n_threads, sizeof(pthread_t));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
samtools/bam_sort.c:420:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
w[i].buf_len = rest / (n_threads - i);
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bam_sort.c:462:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
max_mem = _max_mem * n_threads;
˜ ^˜˜˜˜˜˜˜˜
samtools/bam_sort.c:486:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = realloc(b->data, b->m_data);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bam_sort.c:488:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays
˜ ˜˜˜^˜˜˜˜˜
samtools/bam_sort.c:512:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fns = (char**)calloc(n_files, sizeof(char*));
˜˜˜˜˜˜ ^˜˜˜˜˜˜
32 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/sam_header.c -o samtools/sam_header.o
In file included from samtools/sam_header.c:9:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools/sam_header.c:163:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*lineptr = malloc(len);
˜˜˜˜˜˜ ^˜˜
samtools/sam_header.c:164:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*n = len;
˜ ^˜˜
samtools/sam_header.c:168:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*lineptr = realloc(*lineptr, len);
˜˜˜˜˜˜˜ ^˜˜
samtools/sam_header.c:169:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*n = len;
˜ ^˜˜
samtools/sam_header.c:150:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
len = to - text + 1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/sam_header.c:191:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tag->value = malloc(len+1);
˜˜˜˜˜˜ ˜˜˜^˜
samtools/sam_header.c:187:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int len = value_to-value_from+1;
˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
samtools/sam_header.c:542:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
out = malloc(len+1);
˜˜˜˜˜˜ ˜˜˜^˜
samtools/sam_header.c:664:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ret = realloc(ret, max * sizeof(void*));
^˜˜ ˜
samtools/sam_header.c:715:12: warning: operand of ? changes signedness: 'khint_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
return h? kh_size(tbl) : 0;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
./samtools/khash.h:471:26: note: expanded from macro 'kh_size'
#define kh_size(h) ((h)->size)
˜˜˜˜˜^˜˜˜
samtools/sam_header.c:794:56: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
out = (char**) realloc(out, sizeof(char*)*(nout+1)*ntags);
˜ ˜˜˜˜^˜
samtools/sam_header.c:794:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
out = (char**) realloc(out, sizeof(char*)*(nout+1)*ntags);
˜^˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bam_reheader.c -o samtools/bam_reheader.o
In file included from samtools/bam_reheader.c:5:
./samtools/bam.h:746:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
data = (uint8_t*)realloc(data, m_data);
˜˜˜˜˜˜˜ ^˜˜˜˜˜
./samtools/bam.h:767:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->data = (uint8_t*)calloc(b->data_len, 1);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
samtools/bam_reheader.c:21:41: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
samtools/bam_reheader.c:26:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(buf, 1, len, fp->fp);
˜˜˜˜˜˜ ^˜˜
samtools/bam_reheader.c:25:16: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c:44:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
kpa_par_t kpa_par_def = { 0.001, 0.1, 10 };
˜ ^˜˜˜˜
samtools/kprobaln.c:44:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
kpa_par_t kpa_par_def = { 0.001, 0.1, 10 };
˜ ^˜˜
samtools/kprobaln.c:45:27: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
kpa_par_t kpa_par_alt = { 0.0001, 0.01, 10 };
˜ ^˜˜˜˜˜
samtools/kprobaln.c:45:35: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
kpa_par_t kpa_par_alt = { 0.0001, 0.01, 10 };
˜ ^˜˜˜
samtools/kprobaln.c:90:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
f = calloc(l_query+1, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
samtools/kprobaln.c:91:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (is_backward) b = calloc(l_query+1, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
samtools/kprobaln.c:93:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
f[i] = calloc(bw2 * 3 + 6, sizeof(double)); // FIXME: this is over-allocated for very short seqs
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜
samtools/kprobaln.c:94:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (is_backward) b[i] = calloc(bw2 * 3 + 6, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜
samtools/kprobaln.c:96:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = calloc(l_query+2, sizeof(double)); // s[] is the scaling factor to avoid underflow
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
samtools/kprobaln.c:98:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
_qual = calloc(l_query, sizeof(float));
˜˜˜˜˜˜ ^˜˜˜˜˜˜
samtools/kprobaln.c:101:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
g_qual2prob[i] = pow(10, -i/10.);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/kprobaln.c:235:75: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k;
˜ ^
12 warnings generated.
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
In file included from samtools/bcftools/bcf.c:5:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
In file included from samtools/bcftools/bcf.c:6:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
samtools/bcftools/bcf.c:51:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->name = malloc(h->l_nm);
˜˜˜˜˜˜ ˜˜˜^˜˜˜
samtools/bcftools/bcf.c:54:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->sname = malloc(h->l_smpl);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜
samtools/bcftools/bcf.c:57:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->txt = malloc(h->l_txt);
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
samtools/bcftools/bcf.c:79:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
list = calloc(n, sizeof(void*));
˜˜˜˜˜˜ ^
samtools/bcftools/bcf.c:131:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
˜˜˜^˜˜˜ ˜
samtools/bcftools/bcf.c:132:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/bcf.c:132:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/bcf.c:150:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/bcf.c:136:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/bcf.c:184:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->str = realloc(b->str, b->m_str);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
samtools/bcftools/bcf.c:314:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
b->str = realloc(b->str, b->m_str);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
samtools/bcftools/bcf.c:308:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int shift = b->fmt - b->str;
˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
samtools/bcftools/bcf.c:328:33: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len_diff = 0, ori_len = strlen(str);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/bcf.c:366:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l -= nrm;
˜˜ ^˜˜
samtools/bcftools/bcf.c:378:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
r->str = realloc(r->str, r->m_str);
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
27 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
In file included from samtools/bcftools/vcf.c:7:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
In file included from samtools/bcftools/vcf.c:8:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
samtools/bcftools/vcf.c:52:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
res = gzread(vcf->fp.gz, data, length);
˜˜˜˜˜˜ ^˜˜˜˜˜
samtools/bcftools/vcf.c:50:9: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
res = bgzf_read(vcf->fp.bgzf, data, length);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:68:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(vcfFile, vcfFile_read, 4096)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:121:26: note: expanded from macro '__KS_GETUNTIL'
str->m = str->l + (i - ks->begin) + 1; \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:68:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(vcfFile, vcfFile_read, 4096)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:126:25: note: expanded from macro '__KS_GETUNTIL'
str->l = str->l + (i - ks->begin); \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:68:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSTREAM_INIT(vcfFile, vcfFile_read, 4096)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:138:15: note: expanded from macro '__KS_GETUNTIL'
return str->l; \
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bcftools/vcf.c:100:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
samtools/bcftools/vcf.c:107:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
kputsn(p, aux.p - p, &smpl);
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/vcf.c:116:38: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
h->sname = smpl.s; h->l_smpl = smpl.l;
˜ ˜˜˜˜˜^
samtools/bcftools/vcf.c:117:35: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
h->txt = meta.s; h->l_txt = meta.l;
˜ ˜˜˜˜˜^
samtools/bcftools/vcf.c:151:19: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rn.m = rn.l = h->l_nm; rn.s = h->name;
˜ ˜˜˜^˜˜˜
samtools/bcftools/vcf.c:162:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
h->l_nm = rn.l; h->name = rn.s;
˜ ˜˜˜^
samtools/bcftools/vcf.c:194:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/vcf.c:212:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
return v->line.l + 1;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/vcf.c:224:24: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
str.l = 0; str.m = b->m_str; str.s = b->str;
˜ ˜˜˜^˜˜˜˜
samtools/bcftools/vcf.c:225:19: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rn.l = rn.m = h->l_nm; rn.s = h->name;
˜ ˜˜˜^˜˜˜
samtools/bcftools/vcf.c:241:44: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
˜ ^˜˜˜˜˜˜
samtools/bcftools/vcf.c:269:70: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:274:39: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
((uint8_t*)b->gi[i].data)[k-9] = x;
˜ ^
samtools/bcftools/vcf.c:278:40: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
((uint32_t*)b->gi[i].data)[k-9] = x;
˜ ^
samtools/bcftools/vcf.c:282:40: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
((uint16_t*)b->gi[i].data)[k-9] = x;
˜ ^
samtools/bcftools/vcf.c:290:29: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
data[(k-9) * y + j] = x;
˜ ^
samtools/bcftools/vcf.c:298:11: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
x = strtod(q, &q);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:299:38: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
data[(k-9) * y + j] = x > 0? -x/10. : x;
˜ ˜˜^˜˜˜
samtools/bcftools/vcf.c:304:15: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
endblock: i = i;
˜ ^ ˜
samtools/bcftools/vcf.c:244:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->l_str = str.l; b->m_str = str.m; b->str = str.s;
˜ ˜˜˜˜^
samtools/bcftools/vcf.c:244:37: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->l_str = str.l; b->m_str = str.m; b->str = str.s;
˜ ˜˜˜˜^
samtools/bcftools/vcf.c:276:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int x = strtol(q, &q, 10);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:280:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int x = strtol(q, &q, 10);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:288:11: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
x = strtol(q, &q, 10);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/vcf.c:307:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
h->l_nm = rn.l; h->name = rn.s;
˜ ˜˜˜^
samtools/bcftools/vcf.c:309:19: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
return v->line.l + 1;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
43 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
In file included from samtools/bcftools/bcfutils.c:8:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
In file included from samtools/bcftools/bcfutils.c:9:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
In file included from samtools/bcftools/bcfutils.c:10:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
samtools/bcftools/bcfutils.c:70:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
kh_val(hash, k) = kh_size(hash) - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/bcfutils.c:132:55: warning: operand of ? changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *map = malloc(sizeof(int)*(npl>b->n_alleles ? npl : b->n_alleles));
˜ ^˜˜
samtools/bcftools/bcfutils.c:132:64: warning: operand of ? changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int *map = malloc(sizeof(int)*(npl>b->n_alleles ? npl : b->n_alleles));
˜ ˜˜˜^˜˜˜˜˜˜˜˜
samtools/bcftools/bcfutils.c:172:72: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
((uint8_t*)b->gi[igt].data)[i] = ((1<<7|1<<6)>) | map[a1]<<3 | map[a2];
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
samtools/bcftools/bcfutils.c:232:11: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
d1[i] = x;
˜ ^
samtools/bcftools/bcfutils.c:353:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
bcf_append_info(b, str.s, str.l);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^
samtools/bcftools/bcfutils.c:363:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
a = malloc(b->n_smpl * sizeof(int));
˜˜˜^˜˜˜˜˜ ˜
samtools/bcftools/bcfutils.c:373:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
swap = malloc(gi->len * b->n_smpl);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/bcfutils.c:412:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
˜˜˜˜˜˜ ˜˜˜^˜˜˜
samtools/bcftools/bcfutils.c:413:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/bcfutils.c:414:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
h->l_smpl = s.l; h->sname = s.s;
˜ ˜˜^
samtools/bcftools/bcfutils.c:425:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
swap = malloc(gi->len * b->n_smpl);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/bcfutils.c:472:31: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
˜˜˜˜˜˜˜˜ ^
samtools/bcftools/bcfutils.c:495:31: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
˜˜˜˜˜˜˜˜ ^
28 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
In file included from samtools/bcftools/prob1.c:13:
In file included from ./samtools/bcftools/prob1.h:4:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
In file included from samtools/bcftools/prob1.c:14:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
samtools/bcftools/prob1.c:17:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(gzFile, gzread, 16384)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:121:26: note: expanded from macro '__KS_GETUNTIL'
str->m = str->l + (i - ks->begin) + 1; \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/prob1.c:17:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(gzFile, gzread, 16384)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:126:25: note: expanded from macro '__KS_GETUNTIL'
str->l = str->l + (i - ks->begin); \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/prob1.c:17:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSTREAM_INIT(gzFile, gzread, 16384)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:138:15: note: expanded from macro '__KS_GETUNTIL'
return str->l; \
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bcftools/prob1.c:107:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:107:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:114:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
x = strtol(p, &p, 10);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/prob1.c:147:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->ploidy = malloc(n);
˜˜˜˜˜˜ ^
samtools/bcftools/prob1.c:156:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->pdg = calloc(3 * ma->n, sizeof(double));
˜˜˜˜˜˜ ˜˜^˜˜˜˜˜˜
samtools/bcftools/prob1.c:157:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->phi = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:158:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->phi_indel = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:159:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->phi1 = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:160:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->phi2 = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:161:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->z = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:162:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->zswap = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:163:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:164:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->z2 = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:165:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->afs = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:166:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->afs1 = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:167:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ma->lf = calloc(ma->M + 1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:229:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *het_probs = (double*) calloc(rare_copies+1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
samtools/bcftools/prob1.c:288:14: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
˜ ˜˜˜^˜˜˜˜
samtools/bcftools/prob1.c:288:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
˜ ˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:290:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:290:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:328:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:328:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:375:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
_pdg = pdg = malloc(sizeof(double)*ma->n*npdg);
˜˜˜˜˜^
samtools/bcftools/prob1.c:375:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
_pdg = pdg = malloc(sizeof(double)*ma->n*npdg);
˜^˜˜˜
samtools/bcftools/prob1.c:502:14: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
˜ ˜˜˜^˜˜˜˜
samtools/bcftools/prob1.c:502:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
˜ ˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:550:55: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
((uint8_t*)b->gi[old_n_gi].data)[isample] = als;
˜ ^˜˜
samtools/bcftools/prob1.c:551:55: warning: implicit conversion loses integer precision: 'int' to 'uint8_t' (aka 'unsigned char') [-Wconversion]
((uint8_t*)b->gi[old_n_gi+1].data)[isample] = (int)lk;
˜ ^˜˜˜˜˜˜
samtools/bcftools/prob1.c:575:29: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
b->qual = gts>1 ? -4.343*(ref_lk - lk_sum) : -4.343*log(1-exp(ref_lk - lk_sum));
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/prob1.c:575:56: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
b->qual = gts>1 ? -4.343*(ref_lk - lk_sum) : -4.343*log(1-exp(ref_lk - lk_sum));
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/prob1.c:504:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:504:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:623:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:623:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
˜ ˜˜^
samtools/bcftools/prob1.c:633:19: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
p = alloca(b->n_alleles * sizeof(long));
˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/alloca.h:43:31: note: expanded from macro 'alloca'
#define alloca(size) __alloca(size)
^
/usr/include/alloca.h:44:41: note: expanded from macro '__alloca'
#define __alloca(size) __builtin_alloca(size)
^
samtools/bcftools/prob1.c:634:36: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memset(p, 0, sizeof(long) * b->n_alleles);
˜ ˜˜˜^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:634:36: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
memset(p, 0, sizeof(long) * b->n_alleles);
˜ ˜˜˜^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:686:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(z[0], 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:686:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(z[0], 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:687:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(z[1], 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:687:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(z[1], 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:714:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:714:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
samtools/bcftools/prob1.c:760:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:760:65: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
samtools/bcftools/prob1.c:762:56: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
gzwrite(bcf_p1_fp_lk, ma->z, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
samtools/bcftools/prob1.c:770:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:770:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:771:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:771:60: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:775:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:775:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
samtools/bcftools/prob1.c:821:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
p1->hg = calloc(2*n1+1, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜^˜
samtools/bcftools/prob1.c:823:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
p1->hg[k1] = calloc(2*n2+1, sizeof(double));
˜˜˜˜˜˜ ˜˜˜˜^˜
samtools/bcftools/prob1.c:831:9: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
sum = suml;
˜ ^˜˜˜
samtools/bcftools/prob1.c:891:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:891:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
samtools/bcftools/prob1.c:897:35: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
ma->afs1[k] = phi[k] * ma->z[k] / sum;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
samtools/bcftools/prob1.c:905:23: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
*p_var_folded = sum2 / sum;
˜ ˜˜˜˜˜^˜˜˜˜
samtools/bcftools/prob1.c:906:77: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
*p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
samtools/bcftools/prob1.c:912:13: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
return sum / ma->M;
˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
samtools/bcftools/prob1.c:950:23: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
double p = ma->z[k] / sum;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
samtools/bcftools/prob1.c:991:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->afs, 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
samtools/bcftools/prob1.c:991:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(ma->afs, 0, sizeof(double) * (ma->M + 1));
˜ ˜˜˜˜˜˜^˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
80 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/index.c -o samtools/bcftools/index.o
In file included from samtools/bcftools/index.c:6:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
In file included from samtools/bcftools/index.c:7:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
samtools/bcftools/index.c:37:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
samtools/bcftools/index.c:63:26: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t));
˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
samtools/bcftools/index.c:65:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
last_tid = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:66:13: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:66:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:79:14: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
last_off = bgzf_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:76:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
tmp = strlen(b->ref);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:105:21: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t x = idx->n;
˜ ˜˜˜˜˜^
samtools/bcftools/index.c:144:41: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index2 = (bcf_lidx_t*)calloc(idx->n, sizeof(bcf_lidx_t));
˜˜˜˜˜˜ ˜˜˜˜˜^
samtools/bcftools/index.c:151:46: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index2->offset = (uint64_t*)calloc(index2->m, 8);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
samtools/bcftools/index.c:196:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(buf, 1, l, fp);
˜˜˜˜˜˜ ^
samtools/bcftools/index.c:180:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
l = strlen(url);
˜ ^˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:195:14: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:215:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int l = strlen(fnidx);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/index.c:287:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
p = s = (char*)malloc(l+1);
˜˜˜˜˜˜ ˜^˜
samtools/bcftools/index.c:286:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
l = strlen(str);
˜ ^˜˜˜˜˜˜˜˜˜˜
28 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
In file included from samtools/bcftools/bcf2qcall.c:5:
./samtools/bcftools/bcf.h:192:14: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
x = x<<8 | str[i];
˜ ^˜˜˜˜˜
samtools/bcftools/bcf2qcall.c:33:13: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
anno[i] = strtol(p, &p, 10);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
samtools/bcftools/bcf2qcall.c:70:31: warning: arithmetic on a pointer to void is a GNU extension [-Wpointer-arith]
uint8_t *p = b->gi[i0].data + i * b->gi[i0].len;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
3 warnings generated.
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tabix/index.c -o tabix/index.o
In file included from tabix/index.c:4:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
In file included from tabix/index.c:6:
./samtools/kstring.h:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:83:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:88:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->l += l;
˜˜ ^
./samtools/kstring.h:95:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return kputsn(p, strlen(p), s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
./samtools/kstring.h:105:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s->s[s->l++] = c;
˜ ^
./samtools/kstring.h:118:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:119:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:135:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:136:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
./samtools/kstring.h:152:13: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if (s->l + l + 1 >= s->m) {
˜ ^
./samtools/kstring.h:153:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
s->m = s->l + l + 2;
˜ ^
tabix/index.c:22:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSORT_INIT(offt, pair64_t, pair64_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:201:81: note: expanded from macro 'KSORT_INIT'
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
˜^
tabix/index.c:22:1: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
KSORT_INIT(offt, pair64_t, pair64_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:206:31: note: expanded from macro 'KSORT_INIT'
ks_combsort_##name(t - s + 1, s); \
˜˜˜˜˜˜^˜˜
tabix/index.c:22:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT(offt, pair64_t, pair64_lt)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:271:12: note: expanded from macro 'KSORT_INIT'
for (i = n; i > 1; --i) { \
˜ ^
tabix/index.c:114:42: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
idx->index = realloc(idx->index, idx->max * sizeof(void*));
˜˜˜˜˜^˜˜ ˜
tabix/index.c:115:44: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t));
˜˜˜˜˜^˜˜ ˜
tabix/index.c:120:16: warning: implicit conversion changes signedness: 'khint_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
tid = size = kh_size(idx->tname);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/khash.h:471:26: note: expanded from macro 'kh_size'
#define kh_size(h) ((h)->size)
˜˜˜˜˜^˜˜˜
tabix/index.c:175:17: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
line[i] = c;
˜ ^
tabix/index.c:140:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
intv->beg = intv->end = strtol(line + b, &s, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:147:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:174:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
if (s) intv->end = strtol(s, &s, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:200:57: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
*x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
˜ ^
tabix/index.c:202:32: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
intv->bin = ti_reg2bin(intv->beg, intv->end);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
tabix/index.c:202:43: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
intv->bin = ti_reg2bin(intv->beg, intv->end);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜
tabix/index.c:198:35: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^
tabix/index.c:220:19: warning: implicit conversion changes signedness: 'int' to 'khint32_t' (aka 'unsigned int') [-Wsign-conversion]
k = kh_put(i, h, bin, &ret);
˜˜˜˜˜˜˜˜ ^˜˜
./samtools/khash.h:402:48: note: expanded from macro 'kh_put'
#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
^
tabix/index.c:242:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
tabix/index.c:252:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
return (uint64_t)beg<<32 | end;
˜ ^˜˜
tabix/index.c:271:13: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
p->n = m + 1;
˜ ˜˜^˜˜
tabix/index.c:305:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:305:44: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:306:24: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:306:51: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
˜ ^˜˜˜˜˜˜˜˜˜˜
tabix/index.c:311:15: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
last_off = bgzf_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:336:41: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
tabix/index.c:338:31: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
save_bin = last_bin = intv.bin;
˜ ˜˜˜˜˜^˜˜
tabix/index.c:347:14: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
last_off = bgzf_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:350:57: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
tabix/index.c:350:77: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:354:23: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int' [-Wsign-conversion]
int i, beg = offset0>>32, end = offset0&0xffffffffu;
˜˜˜ ˜˜˜˜˜˜˜^˜˜˜
tabix/index.c:354:42: warning: implicit conversion changes signedness: 'unsigned long long' to 'int' [-Wsign-conversion]
int i, beg = offset0>>32, end = offset0&0xffffffffu;
˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:401:21: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t x = idx->n;
˜ ˜˜˜˜˜^
tabix/index.c:422:44: warning: implicit conversion changes signedness: 'unsigned long' to 'ssize_t' (aka 'long') [-Wsign-conversion]
bgzf_write(fp, name[i], strlen(name[i]) + 1);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
tabix/index.c:429:10: warning: implicit conversion changes signedness: 'khint_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
size = kh_size(index);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/khash.h:471:26: note: expanded from macro 'kh_size'
#define kh_size(h) ((h)->size)
˜˜˜˜˜^˜˜˜
tabix/index.c:431:17: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t x = size;
˜ ^˜˜˜
tabix/index.c:492:41: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜˜^
tabix/index.c:493:40: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
˜˜˜˜˜˜ ˜˜˜˜˜^
tabix/index.c:511:16: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
buf = calloc(l, 1);
˜˜˜˜˜˜ ^
tabix/index.c:556:46: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index2->offset = (uint64_t*)calloc(index2->m, 8);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^
tabix/index.c:601:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite(buf, 1, l, fp);
˜˜˜˜˜˜ ^
tabix/index.c:585:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
l = strlen(url);
˜ ^˜˜˜˜˜˜˜˜˜˜
tabix/index.c:600:14: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:620:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int l = strlen(fnidx);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:641:22: warning: implicit conversion changes signedness: 'const int32_t' (aka 'const int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
names = calloc(idx->n, sizeof(void*));
˜˜˜˜˜˜ ˜˜˜˜˜^
tabix/index.c:710:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
p = s = (char*)malloc(l+1);
˜˜˜˜˜˜ ˜^˜
tabix/index.c:709:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
l = strlen(str);
˜ ^˜˜˜˜˜˜˜˜˜˜
tabix/index.c:750:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
˜ ^
tabix/index.c:751:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
˜ ^
tabix/index.c:752:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
˜ ^
tabix/index.c:753:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
˜ ^
tabix/index.c:754:69: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
˜ ^
tabix/index.c:783:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
n_bins = reg2bins(beg, end, bins);
˜˜˜˜˜˜˜˜ ^˜˜
tabix/index.c:783:25: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
n_bins = reg2bins(beg, end, bins);
˜˜˜˜˜˜˜˜ ^˜˜
tabix/index.c:803:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
off = (pair64_t*)calloc(n_off, 16);
˜˜˜˜˜˜ ^˜˜˜˜
tabix/index.c:818:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ks_introsort(offt, n_off, off);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./samtools/ksort.h:279:54: note: expanded from macro 'ks_introsort'
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
^
tabix/index.c:859:40: warning: implicit conversion changes signedness: 'uint64_t' (aka 'unsigned long long') to 'int64_t' (aka 'long long') [-Wsign-conversion]
bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^
tabix/index.c:860:22: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
iter->curr_off = bgzf_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:866:21: warning: implicit conversion changes signedness: 'long long' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
iter->curr_off = bgzf_tell(fp);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/bgzf.h:127:51: note: expanded from macro 'bgzf_tell'
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
tabix/index.c:848:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (len) *len = iter->str.l;
˜ ˜˜˜˜˜˜˜˜˜˜^
tabix/index.c:871:31: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (len) *len = iter->str.l;
˜ ˜˜˜˜˜˜˜˜˜˜^
72 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c tabix/bedidx.c -o tabix/bedidx.o
tabix/bedidx.c:8:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSORT_INIT_GENERIC(uint64_t)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:292:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:201:81: note: expanded from macro 'KSORT_INIT'
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
˜^
tabix/bedidx.c:8:1: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
KSORT_INIT_GENERIC(uint64_t)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:292:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:206:31: note: expanded from macro 'KSORT_INIT'
ks_combsort_##name(t - s + 1, s); \
˜˜˜˜˜˜^˜˜
tabix/bedidx.c:8:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSORT_INIT_GENERIC(uint64_t)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:292:36: note: expanded from macro 'KSORT_INIT_GENERIC'
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/ksort.h:271:12: note: expanded from macro 'KSORT_INIT'
for (i = n; i > 1; --i) { \
˜ ^
tabix/bedidx.c:11:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(gzFile, gzread, 8192)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:121:26: note: expanded from macro '__KS_GETUNTIL'
str->m = str->l + (i - ks->begin) + 1; \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
tabix/bedidx.c:11:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSTREAM_INIT(gzFile, gzread, 8192)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:126:25: note: expanded from macro '__KS_GETUNTIL'
str->l = str->l + (i - ks->begin); \
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
tabix/bedidx.c:11:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSTREAM_INIT(gzFile, gzread, 8192)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./samtools/kseq.h:138:15: note: expanded from macro '__KS_GETUNTIL'
return str->l; \
˜˜˜˜˜˜ ˜˜˜˜˜^
In file included from tabix/bedidx.c:19:
./samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
khint_t h = *s;
˜ ^˜
./samtools/khash.h:339:48: warning: implicit conversion changes signedness: 'const char' to 'unsigned int' [-Wsign-conversion]
if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
˜ ^˜
tabix/bedidx.c:37:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
idx = realloc(idx, m * sizeof(int));
^ ˜
tabix/bedidx.c:59:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ks_introsort(uint64_t, p->n, p->a);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^
./samtools/ksort.h:279:54: note: expanded from macro 'ks_introsort'
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
^
tabix/bedidx.c:132:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
p->a = realloc(p->a, p->m * 8);
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜
tabix/bedidx.c:134:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
p->a[p->n++] = (uint64_t)beg<<32 | end;
˜ ^˜˜
12 warnings generated.
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc"
cp ../Rsamtools.mk "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc"
mkdir -p "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib"
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o utilities.o zip_compression.o -pthread /Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/libbam.a /Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/libbcf.a /Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsamtools)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsamtools.buildbin-libdir/Rsamtools/libs//Rsamtools.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs//Rsamtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs//Rsamtools.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs//Rsamtools.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs//Rsamtools.so"