Package: ShortRead

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ShortRead_1.18.0.tar.gz

StartedAt: 2013-05-01 10:53:07 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:59:55 -0700 (Wed, 01 May 2013)

EllapsedTime: 408.0 seconds

RetCode: 0

Status:  OK

CheckDir: ShortRead.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ShortRead.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 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.18.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* 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 'ShortRead' can be installed ... [38s/41s] 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 ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
.readQual: no visible global function definition for 'readFASTA'
flag,QAReadQuality: no visible binding for global variable 'Score'
flag,QAReadQuality: no visible binding for global variable 'Id'
flag,QAReadQuality: no visible binding for global variable 'Density'
report,QAFrequentSequence: no visible binding for global variable
  'TopCount'
report,QAFrequentSequence: no visible binding for global variable 'Id'
report,QANucleotideByCycle: no visible binding for global variable
  'Base'
report,QANucleotideUse: no visible binding for global variable
  'Nucleotide'
report,QAQualityUse: no visible binding for global variable 'Count'
report,QAQualityUse: no visible binding for global variable 'Id'
report,QAQualityUse: no visible binding for global variable 'Quality'
report,QAReadQuality: no visible binding for global variable 'Id'
report,QASequenceUse: no visible binding for global variable
  'Occurrences'
report,QASequenceUse: no visible binding for global variable 'Id'
report,QASequenceUse: no visible binding for global variable 'Reads'
* 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 ... [49s/51s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
Snapshot-class 13.794  0.581  15.067
qa2             7.583  0.223   8.206
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'ShortRead_unit_tests.R' [65s/66s]
 [65s/66s] 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck/00check.log'
for details.

* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_ShortRead.c -o R_init_ShortRead.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c alphabet.c -o alphabet.o
alphabet.c:31:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
                    ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
alphabet.c:31:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
                    ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
alphabet.c:39:13: warning: variable length array folded to constant array as an extension [-Wpedantic]
    int map[MAX_MAP];
            ^˜˜˜˜˜˜
alphabet.c:96:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
                    ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
alphabet.c:96:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(ansp, 0, LENGTH(ans) * sizeof(int)); /* initialize to 0 */
                    ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
alphabet.c:106:14: warning: variable length array folded to constant array as an extension [-Wpedantic]
    int map1[MAX_MAP], map2[MAX_MAP];
             ^˜˜˜˜˜˜
alphabet.c:106:29: warning: variable length array folded to constant array as an extension [-Wpedantic]
    int map1[MAX_MAP], map2[MAX_MAP];
                            ^˜˜˜˜˜˜
alphabet.c:232:32: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    size_t len = diff < 0 ? ra.length : rb.length;
           ˜˜˜              ˜˜˜^˜˜˜˜˜
alphabet.c:232:44: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    size_t len = diff < 0 ? ra.length : rb.length;
           ˜˜˜                          ˜˜˜^˜˜˜˜˜
alphabet.c:243:32: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    size_t len = diff < 0 ? ra.length : rb.length;
           ˜˜˜              ˜˜˜^˜˜˜˜˜
alphabet.c:243:44: warning: operand of ? changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    size_t len = diff < 0 ? ra.length : rb.length;
           ˜˜˜                          ˜˜˜^˜˜˜˜˜
alphabet.c:258:17: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(xptr, len, sizeof(XSort), stable_compare_cachedCharSeq);
    ˜˜˜˜˜       ^˜˜
alphabet.c:268:37: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    XSort *xptr = (XSort *) R_alloc(len, sizeof(XSort));
                            ˜˜˜˜˜˜˜ ^˜˜
alphabet.c:288:37: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    XSort *xptr = (XSort *) R_alloc(len, sizeof(XSort));
                            ˜˜˜˜˜˜˜ ^˜˜
alphabet.c:311:37: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    XSort *xptr = (XSort *) R_alloc(len, sizeof(XSort));
                            ˜˜˜˜˜˜˜ ^˜˜
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io.c -o io.o
io.c:39:22: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
            buf[j] = decode(roSeq.seq[j]);
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:111:14: warning: variable length array folded to constant array as an extension [-Wpedantic]
    char buf[LINEBUF_SIZE + 1];
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:115:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    while (*n_cycles == 0 && (bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
                                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:117:56: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        while ((p = memchr(p, '\n', (buf + bytes_read) - p))) {
                    ˜˜˜˜˜˜          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
io.c:128:57: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    while ((p = memchr(p, CYCLE_END, (buf + bytes_read) - p))) {
                ˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
io.c:132:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:134:61: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        while ((p = memchr(p, CYCLE_END, (buf + bytes_read) - p))) {
                    ˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
io.c:224:36: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
            score[cycle++] = qbase + ((char) v[0] > v[2] ? v[0] : v[2]);
                           ˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:550:38: warning: variable length array folded to constant array as an extension [-Wpedantic]
    char linebuf[LINEBUF_SIZE], *elt[N_FIELDS];
                                     ^˜˜˜˜˜˜˜
io.c:713:18: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
        withId = LOGICAL(withFlags)[0],
        ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:714:30: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
        withMultiplexIndex = LOGICAL(withFlags)[1],
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io.c:715:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
        withPairedReadNumber = LOGICAL(withFlags)[2];
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io_bowtie.c -o io_bowtie.o
io_bowtie.c:21:38: warning: variable length array folded to constant array as an extension [-Wpedantic]
    char linebuf[LINEBUF_SIZE], *elt[N_FIELDS];
                                     ^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c io_soap.c -o io_soap.o
io_soap.c:22:38: warning: variable length array folded to constant array as an extension [-Wpedantic]
    char linebuf[LINEBUF_SIZE], *elt[N_FIELDS];
                                     ^˜˜˜˜˜˜˜
io_soap.c:22:38: note: initializer of 'N_FIELDS' is not a constant expression
io_soap.c:20:15: note: declared here
    const int N_FIELDS = N_ELTS;
              ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c pileup.c -o pileup.o
pileup.c:13:29: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
    memset(INTEGER(res), 0, length(res) * sizeof(int));
                            ^˜˜˜˜˜˜˜˜˜˜ ˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1029:20: note: expanded from macro 'length'
#define length(x)               Rf_length(x)
                                ^˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
pileup.c:13:29: warning: implicit conversion changes signedness: 'R_len_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
    memset(INTEGER(res), 0, length(res) * sizeof(int));
                            ^˜˜˜˜˜˜˜˜˜˜ ˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1029:20: note: expanded from macro 'length'
#define length(x)               Rf_length(x)
                                ^˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc:35:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      (void) fread( seq_name, sizeof(char), name_len, fp );
             ˜˜˜˜˜                          ^˜˜˜˜˜˜˜
readBfaToc.cc:41:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      fseek( fp, 2 * sizeof(bit64_t) * seq_len, SEEK_CUR);
                                     ˜ ^˜˜˜˜˜˜
readBfaToc.cc:47:40: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
   PROTECT( res = allocVector( INTSXP, seqs.size() ) );   
                  ˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
readBfaToc.cc:48:42: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
   PROTECT( names = allocVector( STRSXP, seqs.size() ) );   
                    ˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c read_maq_map.cc -o read_maq_map.o
read_maq_map.cc:128:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        INTEGER(seq   )[i] = read.seqid + 1;
                           ˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
read_maq_map.cc:180:14: note: in instantiation of function template specialization 'read_maq_map_B<128>' requested here
      return read_maq_map_B< MAX_READLEN_NEW >( filename, maxreads );
             ^
read_maq_map.cc:80:32: warning: implicit conversion loses integer precision: 'bit64_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        actnreads = mapheader->n_mapped_reads;
                  ˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from read_maq_map.cc:13:
./maqmap_m.h:106:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    mm->ref_name = (char **) calloc(mm->n_ref, sizeof(char *));
                             ˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
read_maq_map.cc:73:18: note: in instantiation of function template specialization 'maqmap_read_header<128>' requested here
    mapheader =  maqmap_read_header<max_readlen>( mapfile );   
                 ^
read_maq_map.cc:180:14: note: in instantiation of function template specialization 'read_maq_map_B<128>' requested here
      return read_maq_map_B< MAX_READLEN_NEW >( filename, maxreads );
             ^
In file included from read_maq_map.cc:13:
./maqmap_m.h:109:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        mm->ref_name[k] = (char *) malloc(len * sizeof(char));
                                          ^˜˜ ˜
./maqmap_m.h:110:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        gzread(fp, mm->ref_name[k], len);
        ˜˜˜˜˜˜                      ^˜˜
read_maq_map.cc:128:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        INTEGER(seq   )[i] = read.seqid + 1;
                           ˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜
read_maq_map.cc:182:14: note: in instantiation of function template specialization 'read_maq_map_B<64>' requested here
      return read_maq_map_B< MAX_READLEN_OLD >( filename, maxreads );
             ^
read_maq_map.cc:80:32: warning: implicit conversion loses integer precision: 'bit64_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        actnreads = mapheader->n_mapped_reads;
                  ˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from read_maq_map.cc:13:
./maqmap_m.h:106:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    mm->ref_name = (char **) calloc(mm->n_ref, sizeof(char *));
                             ˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
read_maq_map.cc:73:18: note: in instantiation of function template specialization 'maqmap_read_header<64>' requested here
    mapheader =  maqmap_read_header<max_readlen>( mapfile );   
                 ^
read_maq_map.cc:182:14: note: in instantiation of function template specialization 'read_maq_map_B<64>' requested here
      return read_maq_map_B< MAX_READLEN_OLD >( filename, maxreads );
             ^
In file included from read_maq_map.cc:13:
./maqmap_m.h:109:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        mm->ref_name[k] = (char *) malloc(len * sizeof(char));
                                          ^˜˜ ˜
./maqmap_m.h:110:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        gzread(fp, mm->ref_name[k], len);
        ˜˜˜˜˜˜                      ^˜˜
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sampler.c -o sampler.o
sampler.c:135:44: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memcpy((char *) x.seq, start, (buf - start) * sizeof(Rbyte));
                                       ˜˜˜˜^˜˜˜˜˜˜  ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:135:44: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
        memcpy((char *) x.seq, start, (buf - start) * sizeof(Rbyte));
                                       ˜˜˜˜^˜˜˜˜˜˜  ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:143:37: warning: implicit conversion changes signedness: 'const Rbyte' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                *curr++ = DNAencode(*buf++);
                          ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
sampler.c:159:27: warning: implicit conversion changes signedness: 'const Rbyte' (aka 'const unsigned char') to 'char' [-Wsign-conversion]
                *curr++ = *buf++;
                        ˜ ^˜˜˜˜˜
sampler.c:92:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        id_w[i] = buf - start;
                ˜ ˜˜˜˜^˜˜˜˜˜˜
sampler.c:232:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(intern_record, record, len * sizeof(Rbyte));
                                  ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:232:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(intern_record, record, len * sizeof(Rbyte));
                                  ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:245:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int j = (n - i) * unif_rand();
            ˜   ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
sampler.c:259:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    int n_samp = rbinom(n_curr, n_choose / n_tot);
        ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:312:17: note: expanded from macro 'rbinom'
#define rbinom          Rf_rbinom
                        ^
sampler.c:299:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(sample->records, sample->n_curr,
    ˜˜˜˜˜                  ˜˜˜˜˜˜˜˜^˜˜˜˜˜
sampler.c:310:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(bytes, record, len * sizeof(Rbyte));
                              ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:310:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(bytes, record, len * sizeof(Rbyte));
                              ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:348:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(buf, scratch->bytes, scratch->len * sizeof(Rbyte));
                                    ˜˜˜˜˜˜˜˜˜^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:348:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(buf, scratch->bytes, scratch->len * sizeof(Rbyte));
                                    ˜˜˜˜˜˜˜˜˜^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:350:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(buf + scratch->len, RAW(bin), len * sizeof(Rbyte));
                                             ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:350:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(buf + scratch->len, RAW(bin), len * sizeof(Rbyte));
                                             ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:356:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(buf, RAW(bin), buflen * sizeof(Rbyte));
                              ^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:356:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(buf, RAW(bin), buflen * sizeof(Rbyte));
                              ^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:380:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tail, buf, len * sizeof(Rbyte));
                          ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:380:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tail, buf, len * sizeof(Rbyte));
                          ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:372:41: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        _sampler_add(sampler, prev, buf - prev);
        ˜˜˜˜˜˜˜˜˜˜˜˜                ˜˜˜˜^˜˜˜˜˜
sampler.c:378:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        int len = bufend - buf;
            ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜
sampler.c:500:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(scratch->bytes, RAW(bin), len * sizeof(Rbyte));
                                         ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:500:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(scratch->bytes, RAW(bin), len * sizeof(Rbyte));
                                         ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:505:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(bytes, scratch->bytes, buflen * sizeof(Rbyte));
                                      ^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:505:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(bytes, scratch->bytes, buflen * sizeof(Rbyte));
                                      ^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:506:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(bytes + buflen, RAW(bin), len * sizeof(Rbyte));
                                         ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:506:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(bytes + buflen, RAW(bin), len * sizeof(Rbyte));
                                         ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:540:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tail, buf, len * sizeof(Rbyte));
                          ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
sampler.c:540:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(tail, buf, len * sizeof(Rbyte));
                          ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
sampler.c:526:45: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            _streamer_add(stream, prev, buf - prev);
            ˜˜˜˜˜˜˜˜˜˜˜˜˜               ˜˜˜˜^˜˜˜˜˜
sampler.c:538:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        int len = bufend - buf;
            ˜˜˜   ˜˜˜˜˜˜˜^˜˜˜˜
32 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c trim.c -o trim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c util.c -o util.o
util.c:257:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    i = strlen(linebuf) - 1;
      ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
util.c:281:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        tmp = linebuf[len - i - 1];
                          ˜ ^
util.c:282:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        linebuf[len - i - 1] = linebuf[i];
                    ˜ ^
util.c:342:14: warning: variable length array folded to constant array as an extension [-Wpedantic]
    char buf[LINEBUF_SIZE + 1];
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
util.c:345:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
util.c:347:56: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        while ((p = memchr(p, '\n', (buf + bytes_read) - p))) {
                    ˜˜˜˜˜˜          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c xsnap.c -o xsnap.o
xsnap.c:70:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    int offset = node->curr - node->buf;
        ˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
xsnap.c:82:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    const int n_raw = node->curr - node->buf;
              ˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
xsnap.c:93:24: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
            node->curr - (node->buf + offset[node->n - 1]);
            ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xsnap.c:127:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int w = strlen(s);
        ˜   ^˜˜˜˜˜˜˜˜
4 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 ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ShortRead.Rcheck/ShortRead/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 (ShortRead)

name	user	system	elapsed
AlignedRead-class	0.870	0.021	0.910
BAMQA-class	0.007	0.003	0.011
BowtieQA-class	0.007	0.002	0.009
ExperimentPath-class	0.006	0.003	0.009
FastqQA-class	0.007	0.002	0.010
GappedReads-class	0.351	0.024	0.430
Intensity-class	0.431	0.024	0.455
MAQMapQA-class	0.009	0.001	0.010
QA-class	0.015	0.002	0.017
QualityScore-class	0.025	0.004	0.029
QualityScore	0.026	0.002	0.028
RochePath-class	0.015	0.002	0.016
RocheSet-class	0.012	0.001	0.013
RtaIntensity-class	0.112	0.001	0.114
RtaIntensity	0.054	0.002	0.056
SRFilter-class	0.008	0.001	0.009
SRFilterResult-class	0.098	0.002	0.100
SRSet-class	0.011	0.002	0.013
SRUtil-class	0.329	0.006	0.334
Sampler-class	1.574	0.054	1.649
ShortRead-class	0.126	0.017	0.146
ShortReadQ-class	0.377	0.059	0.439
Snapshot-class	13.794	0.581	15.067
SnapshotFunction-class	0.004	0.006	0.011
SolexaExportQA-class	0.021	0.011	0.033
SolexaIntensity-class	0.262	0.030	0.296
SolexaPath-class	0.195	0.024	0.222
SolexaSet-class	0.163	0.017	0.180
SpTrellis-class	1.555	0.041	1.633
accessors	0.010	0.008	0.018
alphabetByCycle	0.046	0.020	0.067
clean	0.004	0.004	0.009
countLines	0.018	0.013	0.032
deprecated	0.005	0.007	0.013
dotQA-class	0.004	0.005	0.009
dustyScore	0.605	0.014	0.625
polyn	0.009	0.003	0.012
qa	0.565	0.019	0.585
qa2	7.583	0.223	8.206
readAligned	0.450	0.028	0.482
readBaseQuality	0.053	0.009	0.066
readFasta	0.152	0.024	0.195
readFastq	0.153	0.018	0.180
readIntensities	0.181	0.032	0.213
readPrb	0.082	0.020	0.103
readQseq	0.024	0.008	0.032
readXStringColumns	0.166	0.020	0.191
renew	0.129	0.025	0.155
report	0.012	0.007	0.018
spViewPerFeature	2.657	0.082	2.779
srFilter	0.668	0.030	0.707
srapply	0.014	0.007	0.022
srdistance	0.587	0.015	0.602
srduplicated	0.106	0.016	0.132
tables	0.192	0.012	0.209
trimTails	0.070	0.015	0.086