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Package 568/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rsamtools 1.12.2
Bioconductor Package Maintainer
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Rsamtools
Last Changed Rev: 75729 / Revision: 76155
Last Changed Date: 2013-04-16 21:36:57 -0700 (Tue, 16 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: Rsamtools
Version: 1.12.2
Command: rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsamtools_1.12.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rsamtools.buildbin-libdir
StartedAt: 2013-05-01 12:52:14 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:52:52 -0700 (Wed, 01 May 2013)
EllapsedTime: 37.9 seconds
RetCode: 0
Status:  OK 
PackageFile: Rsamtools_1.12.2.tgz
PackageFileSize: 3.655 MiB

Command output

>>>>>>> 
>>>>>>> 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)&gt) | 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"