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Package 513/671HostnameOS / ArchBUILDCHECKBUILD BIN
QuasR 1.0.0
Michael Stadler
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/QuasR
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 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: 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

Command output

* 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

QuasR.Rcheck/00install.out:

* 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)

QuasR.Rcheck/QuasR-Ex.timings:

nameusersystemelapsed
QuasR-package0.0070.0060.013
alignmentStats0.0130.0040.018
preprocessReads3.6120.1703.943
qAlign0.0040.0040.008
qCount 5.144 0.63838.708
qExportWig 0.293 0.05020.557
qMeth 4.134 0.59239.011
qProfile0.8780.0671.015
qProject-class 0.840 0.30318.496
qQCReport2.5590.1222.725