Package: QuasR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch QuasR_1.0.0.tar.gz

StartedAt: 2013-05-01 09:45:44 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:07:15 -0700 (Wed, 01 May 2013)

EllapsedTime: 1290.6 seconds

RetCode: 0

Status:  OK

CheckDir: QuasR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/QuasR.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'QuasR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuasR' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'QuasR' can be installed ... [42s/43s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [36s/143s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
qCount         5.144  0.638  38.708
qMeth          4.134  0.592  39.011
qProject-class 0.840  0.303  18.496
qExportWig     0.293  0.050  20.557
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'QuasR_unit_tests.R' [4m/13m]
 [4m/13m] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'QuasR' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_init_QuasR.cpp -o R_init_QuasR.o
In file included from R_init_QuasR.cpp:4:
In file included from ./merge_reorder_sam.h:13:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
        ˜˜˜˜˜˜                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(b->data, src->data, b->data_len);
        ˜˜˜˜˜˜                     ˜˜˜^˜˜˜˜˜˜˜
In file included from R_init_QuasR.cpp:15:
In file included from ./idxstats_bam.h:5:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:111:18: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
#if ULONG_MAX == ULLONG_MAX
                 ^
/usr/include/i386/limits.h:84:20: note: expanded from macro 'ULLONG_MAX'
#define ULLONG_MAX      0xffffffffffffffffULL   /* max unsigned long long */
                        ^
In file included from R_init_QuasR.cpp:15:
In file included from ./idxstats_bam.h:5:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
        khint_t h = *s;
                ˜   ^˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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 R_init_QuasR.cpp:15:
In file included from ./idxstats_bam.h:7:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam_endian.h:32:12: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
                  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam_endian.h:33:12: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
                  ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam_endian.h:33:50: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
                                                        ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam_endian.h:34:15: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
                     ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam_endian.h:34:52: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
        return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
                                                          ^
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c cat_bam.c -o cat_bam.o
In file included from cat_bam.c:64:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
cat_bam.c:109:51: 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);
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
cat_bam.c:126:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                fwrite(ebuf, 1, len, fp_file);
                ˜˜˜˜˜˜          ^˜˜
cat_bam.c:133:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                fwrite(buf, 1, len, fp_file);
                ˜˜˜˜˜˜         ^˜˜
cat_bam.c:116:23: 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) {
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
In file included from convert_reads_id_bis_rc.c:2:
In file included from ./utilities.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
convert_reads_id_bis_rc.c:4:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:221:2: note: expanded from macro 'KSEQ_INIT2'
        KSTREAM_INIT(type_t, __read, 16384)                     \
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
        __KS_GETUNTIL(__read, __bufsize)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:121:26: note: expanded from macro '__KS_GETUNTIL'
                                str->m = str->l + (i - ks->begin) + 1;                                  \
                                                ˜  ˜˜^˜˜˜˜˜˜˜˜˜˜
convert_reads_id_bis_rc.c:4:1: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:221:2: note: expanded from macro 'KSEQ_INIT2'
        KSTREAM_INIT(type_t, __read, 16384)                     \
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
        __KS_GETUNTIL(__read, __bufsize)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:126:25: note: expanded from macro '__KS_GETUNTIL'
                        str->l = str->l + (i - ks->begin);                                                      \
                                        ˜  ˜˜^˜˜˜˜˜˜˜˜˜˜
convert_reads_id_bis_rc.c:4:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:221:2: note: expanded from macro 'KSEQ_INIT2'
        KSTREAM_INIT(type_t, __read, 16384)                     \
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT'
        __KS_GETUNTIL(__read, __bufsize)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:138:15: note: expanded from macro '__KS_GETUNTIL'
                return str->l;                                                                                                  \
                ˜˜˜˜˜˜ ˜˜˜˜˜^
convert_reads_id_bis_rc.c:4:1: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:224:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_READ(SCOPE)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:190:31: note: expanded from macro '__KSEQ_READ'
                        seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
                                                 ˜ ^
convert_reads_id_bis_rc.c:4:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:224:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_READ(SCOPE)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:200:33: note: expanded from macro '__KSEQ_READ'
                if (c != '+') return seq->seq.l; /* FASTA */ \
                              ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^
convert_reads_id_bis_rc.c:4:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
KSEQ_INIT(gzFile, gzread)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:224:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_READ(SCOPE)
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/kseq.h:210:19: note: expanded from macro '__KSEQ_READ'
                return seq->seq.l; \
                ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^
convert_reads_id_bis_rc.c:60:57: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        translate[(int)from - offset + 'a' -offset] = to + 'a' -offset; // convert small letter
                                                    ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
convert_reads_id_bis_rc.c:82:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            _complement(seq->seq.s, seq->seq.l);
            ˜˜˜˜˜˜˜˜˜˜˜             ˜˜˜˜˜˜˜˜˜^
convert_reads_id_bis_rc.c:83:43: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            _reverse(seq->seq.s, seq->seq.l);
            ˜˜˜˜˜˜˜˜             ˜˜˜˜˜˜˜˜˜^
convert_reads_id_bis_rc.c:84:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            _reverse(seq->qual.s, seq->qual.l);
            ˜˜˜˜˜˜˜˜              ˜˜˜˜˜˜˜˜˜˜^
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c count_alignments.c -o count_alignments.o
In file included from count_alignments.c:12:
In file included from ./count_alignments.h:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c count_alignments_subregions.c -o count_alignments_subregions.o
In file included from count_alignments_subregions.c:12:
In file included from ./count_alignments_subregions.h:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c count_junctions.cpp -o count_junctions.o
In file included from count_junctions.cpp:1:
In file included from ./count_junctions.h:7:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
        ˜˜˜˜˜˜                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(b->data, src->data, b->data_len);
        ˜˜˜˜˜˜                     ˜˜˜^˜˜˜˜˜˜˜
count_junctions.cpp:201:6: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        n = uniqueJunctions.size();
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
count_junctions.cpp:244:6: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        n = jinfo.junctionsU.size();
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c export_wig.c -o export_wig.o
In file included from export_wig.c:4:
In file included from ./export_wig.h:8:
In file included from ./utilities.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
export_wig.c:45:66: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
                        hitPos = bam_calend(&(hit->core), bam1_cigar(hit)) - 1 - tcov->shift;
                               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
export_wig.c:45:74: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        hitPos = bam_calend(&(hit->core), bam1_cigar(hit)) - 1 - tcov->shift;
                                                                               ˜ ˜˜˜˜˜˜^˜˜˜˜
export_wig.c:92:19: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
    tcov->cTlen = bh->target_len[tcov->cTid];
                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
export_wig.c:93:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int32_t' (aka 'int') [-Wconversion]
    tcov->cTbin = ceil((double)(tcov->cTlen) /tcov->bs);
                ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c extract_unmapped_reads.c -o extract_unmapped_reads.o
In file included from extract_unmapped_reads.c:1:
In file included from ./extract_unmapped_reads.h:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
extract_unmapped_reads.c:13:36: 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;
                   ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
extract_unmapped_reads.c:19:24: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        _complement(s, len);
        ˜˜˜˜˜˜˜˜˜˜˜    ^˜˜
extract_unmapped_reads.c:20:21: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        _reverse(s, len);
        ˜˜˜˜˜˜˜˜    ^˜˜
extract_unmapped_reads.c:30:36: 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;
                   ˜˜˜   ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
extract_unmapped_reads.c:34:24: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
        s[i] = bamq[i] + 33;
             ˜ ˜˜˜˜˜˜˜˜^˜˜˜
extract_unmapped_reads.c:36:21: warning: implicit conversion changes signedness: 'const uint32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        _reverse(s, len);
        ˜˜˜˜˜˜˜˜    ^˜˜
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c idxstats_bam.c -o idxstats_bam.o
In file included from idxstats_bam.c:8:
In file included from ./idxstats_bam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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 idxstats_bam.c:8:
In file included from ./idxstats_bam.h:5:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/khash.h:338:14: warning: implicit conversion changes signedness: 'const char' to 'khint_t' (aka 'unsigned int') [-Wsign-conversion]
        khint_t h = *s;
                ˜   ^˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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;
                                                    ˜ ^˜
idxstats_bam.c:77:27: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        INTEGER(reflengths)[i] = header->target_len[i];
                               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
idxstats_bam.c:90:28: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
    INTEGER(unmapped)[i] = (long long)idx->n_no_coor;   
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c merge_reorder_sam.cpp -o merge_reorder_sam.o
In file included from merge_reorder_sam.cpp:1:
In file included from ./merge_reorder_sam.h:13:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
        ˜˜˜˜˜˜                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(b->data, src->data, b->data_len);
        ˜˜˜˜˜˜                     ˜˜˜^˜˜˜˜˜˜˜
merge_reorder_sam.cpp:223:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return queue.size();
    ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
merge_reorder_sam.cpp:277:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            currenttop = mapped[rand() % count];
                                ^˜˜˜˜˜ ˜
merge_reorder_sam.cpp:330:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        numberFlushed = unmapped.size();
                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
merge_reorder_sam.cpp:566:34: warning: implicit conversion changes signedness: 'vector<idLine>::size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
            mapped.erase(mapped.begin()+i);
                         ˜˜˜˜˜˜         ^
merge_reorder_sam.cpp:558:40: warning: implicit conversion loses integer precision: 'vector<idLine>::size_type' (aka 'unsigned long') to 'const int' [-Wshorten-64-to-32]
            locus.insert(pair<string,int>(key,i));
                         ˜˜˜˜                 ^
merge_reorder_sam.cpp:687:22: warning: implicit conversion changes signedness: 'vector<idLine>::size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
            mapped.erase(it+i);
                         ˜˜ ^
merge_reorder_sam.cpp:825:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                n += flush_allele(id, outfh, unmapped, mappedR[rand() % countR], 'R');
                                                       ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
merge_reorder_sam.cpp:831:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                n += flush_allele(id, outfh, unmapped, mappedA[rand() % countA], 'A');
                                                       ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
merge_reorder_sam.cpp:839:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                n += flush_allele(id, outfh, unmapped, mappedR[rand() % countR], 'U');
                                                       ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
merge_reorder_sam.cpp:841:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                n += flush_allele(id, outfh, unmapped, mappedA[rand() % countA], 'U');
                                                       ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
In file included from nucleotide_alignment_frequencies.c:1:
In file included from ./nucleotide_alignment_frequencies.h:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
nucleotide_alignment_frequencies.c:170:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    int end = start + strlen(ref);
              ^˜˜˜˜ ˜
nucleotide_alignment_frequencies.c:210:26: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
    fparam.mm_dist_len = Rf_length(VECTOR_ELT(mmDist,0));
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
nucleotide_alignment_frequencies.c:212:28: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
    fparam.frag_dist_len = Rf_length(VECTOR_ELT(mmDist,2));
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
nucleotide_alignment_frequencies.c:231:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        qsort(fparam.pos_lst, fparam.count_aln, sizeof(char **), compare);
        ˜˜˜˜˜                 ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
nucleotide_alignment_frequencies.c:170:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int end = start + strlen(ref);
        ˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c profile_alignments.c -o profile_alignments.o
In file included from profile_alignments.c:12:
In file included from ./profile_alignments.h:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c quantify_methylation.cpp -o quantify_methylation.o
In file included from quantify_methylation.cpp:5:
In file included from ./quantify_methylation.h:11:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:748:33: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
        ˜˜˜˜˜˜                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/bam.h:768:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(b->data, src->data, b->data_len);
        ˜˜˜˜˜˜                     ˜˜˜^˜˜˜˜˜˜˜
quantify_methylation.cpp:85:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:85:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
                                                                                     ˜˜˜˜˜˜^˜˜˜˜˜
quantify_methylation.cpp:99:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:99:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
                                                                                     ˜˜˜˜˜˜^˜˜˜˜˜
quantify_methylation.cpp:129:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:129:89: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
                                                                                         ˜˜˜˜˜˜^˜˜˜˜˜
quantify_methylation.cpp:140:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:140:89: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
                                                                                         ˜˜˜˜˜˜^˜˜˜˜˜
quantify_methylation.cpp:170:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:170:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
                                                                                     ˜˜˜˜˜˜^˜˜˜˜˜
quantify_methylation.cpp:181:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:181:92: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    for(i=hit->core.pos-cnt->offset, j=0; i<bam_calend(&(hit->core), bam1_cigar(hit))-cnt->offset; i++, j++)
                                                                                     ˜˜˜˜˜˜^˜˜˜˜˜
quantify_methylation.cpp:224:50: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        start = Rf_asInteger(regionStart) - 1, seqlen = strlen(seq), end = 0;
                                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:529:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
            resMatch_int[j] = cntMatch[i];
                            ˜ ^˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:530:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
            resTotal_int[j] = cntTotal[i];
                            ˜ ^˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:437:50: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        start = Rf_asInteger(regionStart) - 1, seqlen = strlen(seq), end = 0;
                                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
quantify_methylation.cpp:586:50: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        start = Rf_asInteger(regionStart) - 1, seqlen = strlen(seq), end = 0;
                                               ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜
21 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
In file included from remove_unmapped_from_sam.c:1:
In file included from ./remove_unmapped_from_sam.h:2:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c split_sam_chr.c -o split_sam_chr.o
In file included from split_sam_chr.c:1:
In file included from ./split_sam_chr.h:2:
In file included from ./utilities.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                            ˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜
split_sam_chr.c:86:69: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  samfile_t **foutList = (samfile_t**)calloc((fin->header->n_targets+1), sizeof(samfile_t*));
                                      ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
split_sam_chr.c:82:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
    fin->header->l_text = strlen(fin->header->text);
                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c utilities.c -o utilities.o
In file included from utilities.c:1:
In file included from ./utilities.h:4:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/sam.h:4:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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);
                                 ˜˜˜˜˜˜˜       ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/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++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o QuasR.so R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o -lz /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -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/QuasR.Rcheck/QuasR/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 (QuasR)

name	user	system	elapsed
QuasR-package	0.007	0.006	0.013
alignmentStats	0.013	0.004	0.018
preprocessReads	3.612	0.170	3.943
qAlign	0.004	0.004	0.008
qCount	5.144	0.638	38.708
qExportWig	0.293	0.050	20.557
qMeth	4.134	0.592	39.011
qProfile	0.878	0.067	1.015
qProject-class	0.840	0.303	18.496
qQCReport	2.559	0.122	2.725