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Package 81/671HostnameOS / ArchBUILDCHECKBUILD BIN
Biostrings 2.28.0
H. Pages
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/Biostrings
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  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: Biostrings
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biostrings_2.28.0.tar.gz
StartedAt: 2013-05-01 02:59:36 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 03:17:34 -0700 (Wed, 01 May 2013)
EllapsedTime: 1078.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Biostrings.Rcheck
Warnings: 3

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.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 'Biostrings/DESCRIPTION' ... OK
* this is package 'Biostrings' version '2.28.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Biostrings' can be installed ... [25s/27s] WARNING
Found the following significant warnings:
  XString_class.c:172:6: warning: variable 'lkup_length' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
See '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00install.out' for details.
* 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 ... WARNING
Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MaskedXString-class.Rd':
  '[IRanges]{Ranges-utils}'

Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/MultipleAlignment-class.Rd':
  '[IRanges:Ranges-utils]{narrow}'

Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00_pkg_src/Biostrings/man/XStringViews-class.Rd':
  '[IRanges:IRanges-setops]{gaps}'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'twoWayAlphabetFrequency'
Undocumented S4 methods:
  generic 'splitAsListReturnedClass' and siglist 'AAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'BStringSet'
  generic 'splitAsListReturnedClass' and siglist 'DNAStringSet'
  generic 'splitAsListReturnedClass' and siglist 'RNAStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XString,XStringSet'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XString'
  generic 'twoWayAlphabetFrequency' and siglist 'XStringSet,XStringSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 ... [14m/14m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
matchPDict-exact      530.181 11.568 559.147
matchPDict-inexact     89.870  3.618 100.940
stringDist             38.284  0.224  42.775
XStringSet-class       14.644  2.162  17.002
XStringSet-io          14.693  1.456  16.491
findPalindromes        14.192  0.110  14.519
PDict-class            13.137  0.541  13.948
matchPWM               11.785  0.082  12.413
matchPattern            9.370  0.359  11.222
XStringSet-comparison   6.785  1.559   8.514
reverseComplement       4.891  0.837   5.839
* 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

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/00check.log'
for details.

Biostrings.Rcheck/00install.out:

* installing *source* package 'Biostrings' ...
** 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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BAB_class.c -o BAB_class.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BitMatrix.c -o BitMatrix.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"   -fPIC  -mtune=native -ggdb -O0 -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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c MIndex_class.c -o MIndex_class.o
MIndex_class.c:192:18: warning: unused variable 'poffsets_order' [-Wunused-variable]
        IntAE poffsets, poffsets_order;
                        ^
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c PreprocessedTB_class.c -o PreprocessedTB_class.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c R_init_Biostrings.c -o R_init_Biostrings.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c RoSeqs_utils.c -o RoSeqs_utils.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c SparseList_utils.c -o SparseList_utils.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c XStringSet_class.c -o XStringSet_class.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c XStringSet_io.c -o XStringSet_io.o
XStringSet_io.c:162:34: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
               seq_data->seq, seq_data->length * sizeof(char));
                              ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
XStringSet_io.c:162:34: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
               seq_data->seq, seq_data->length * sizeof(char));
                              ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
XStringSet_io.c:208:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                dest[j++] = val;
                          ˜ ^˜˜
XStringSet_io.c:244:8: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                            FASTA_comment_markup_length) == 0) {
                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:255:10: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                     FASTA_desc_markup_length) == 0;
                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:227:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        FASTA_comment_markup_length = strlen(FASTA_comment_markup);
                                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:228:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        FASTA_desc_markup_length = strlen(FASTA_desc_markup);
                                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:621:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                    FASTQ_line1_markup_length) != 0) {
                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:645:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                    FASTQ_line3_markup_length) != 0) {
                                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:598:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        FASTQ_line1_markup_length = strlen(FASTQ_line1_markup);
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XStringSet_io.c:599:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        FASTQ_line3_markup_length = strlen(FASTQ_line3_markup);
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c XString_class.c -o XString_class.o
XString_class.c:64:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return code;
        ˜˜˜˜˜˜ ^˜˜˜
XString_class.c:74:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return c;
        ˜˜˜˜˜˜ ^
XString_class.c:92:9: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
        return code;
        ˜˜˜˜˜˜ ^˜˜˜
XString_class.c:141:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                new_buf = (char *) realloc(buf, new_buflength);
                                   ˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:172:6: warning: variable 'lkup_length' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if (lkup == R_NilValue) {
            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:179:30: note: uninitialized use occurs here
                        INTEGER(start)[0], lkup0, lkup_length);
                                                  ^˜˜˜˜˜˜˜˜˜˜
XString_class.c:172:2: note: remove the 'if' if its condition is always false
        if (lkup == R_NilValue) {
        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
XString_class.c:162:17: note: initialize the variable 'lkup_length' to silence this warning
        int lkup_length;
                       ^
                        = 0
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c:31:34: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sco = (int *) R_alloc((long) n1 * n2, sizeof(int));
                      ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜
align_needwunsQS.c:32:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        tra = (char *) R_alloc((long) n1 * n2, sizeof(char));
                       ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜
align_needwunsQS.c:81:29: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        al1_buf = (char *) R_alloc((long) al_buf_size, sizeof(char));
                           ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_needwunsQS.c:82:29: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        al2_buf = (char *) R_alloc((long) al_buf_size, sizeof(char));
                           ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_needwunsQS.c:160:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy((char *) RAW(tag), al1, nal * sizeof(char));
                                       ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_needwunsQS.c:160:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy((char *) RAW(tag), al1, nal * sizeof(char));
                                       ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_needwunsQS.c:166:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy((char *) RAW(tag), al2, nal * sizeof(char));
                                       ^˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_needwunsQS.c:166:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy((char *) RAW(tag), al2, nal * sizeof(char));
                                       ^˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
8 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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
align_pairwiseAlignment.c:135:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                CURR_MATRIX(i, 0) = NEGATIVE_INFINITY;
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:136:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                CURR_MATRIX(i, 1) = NEGATIVE_INFINITY;
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:174:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                        CURR_MATRIX(0, 0) = NEGATIVE_INFINITY;
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:176:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                        CURR_MATRIX(0, 2) = NEGATIVE_INFINITY;
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:256:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align1InfoPtr->mismatch,   0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:256:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align1InfoPtr->mismatch,   0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
align_pairwiseAlignment.c:257:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align2InfoPtr->mismatch,   0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:257:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align2InfoPtr->mismatch,   0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
align_pairwiseAlignment.c:258:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align1InfoPtr->startIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:258:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align1InfoPtr->startIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
align_pairwiseAlignment.c:259:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align2InfoPtr->startIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:259:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align2InfoPtr->startIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
align_pairwiseAlignment.c:260:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align1InfoPtr->widthIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:260:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align1InfoPtr->widthIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
align_pairwiseAlignment.c:261:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align2InfoPtr->widthIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:261:40: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                memset(align2InfoPtr->widthIndel, 0, alignmentBufferSize * sizeof(int));
                                                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
align_pairwiseAlignment.c:273:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                        CURR_MATRIX(0, 0) = NEGATIVE_INFINITY;
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:275:24: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                        CURR_MATRIX(0, 2) = NEGATIVE_INFINITY;
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:578:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        float gapOpeningValue = REAL(gapOpening)[0];
              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:579:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        float gapExtensionValue = REAL(gapExtension)[0];
              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:582:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                gapExtensionValue = NEGATIVE_INFINITY;
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:641:54: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        alignBuffer.currMatrix = (float *) R_alloc((long) 3 * alignmentBufferSize, sizeof(float));
                                           ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:642:54: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        alignBuffer.prevMatrix = (float *) R_alloc((long) 3 * alignmentBufferSize, sizeof(float));
                                           ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:649:43: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                align1Info.mismatch   = (int *) R_alloc((long) alignmentBufferSize, sizeof(int));
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:650:43: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                align2Info.mismatch   = (int *) R_alloc((long) alignmentBufferSize, sizeof(int));
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:651:43: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                align1Info.startIndel = (int *) R_alloc((long) alignmentBufferSize, sizeof(int));
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:652:43: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                align2Info.startIndel = (int *) R_alloc((long) alignmentBufferSize, sizeof(int));
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:653:43: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                align1Info.widthIndel = (int *) R_alloc((long) alignmentBufferSize, sizeof(int));
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:654:43: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                align2Info.widthIndel = (int *) R_alloc((long) alignmentBufferSize, sizeof(int));
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:655:47: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                alignBuffer.sTraceMatrix = (char *) R_alloc((long) nCharProduct, sizeof(char));
                                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:656:47: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                alignBuffer.iTraceMatrix = (char *) R_alloc((long) nCharProduct, sizeof(char));
                                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:657:47: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                alignBuffer.dTraceMatrix = (char *) R_alloc((long) nCharProduct, sizeof(char));
                                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:660:44: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                mismatchBuffer.pattern = (int *) R_alloc((long) mismatchBufferSize, sizeof(int));
                                                 ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:661:44: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                mismatchBuffer.subject = (int *) R_alloc((long) mismatchBufferSize, sizeof(int));
                                                 ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:666:40: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                indel1Buffer.start = (int *) R_alloc((long) indelBufferSize, sizeof(int));
                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:667:40: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                indel1Buffer.width = (int *) R_alloc((long) indelBufferSize, sizeof(int));
                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:670:40: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                indel2Buffer.start = (int *) R_alloc((long) indelBufferSize, sizeof(int));
                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:671:40: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                indel2Buffer.width = (int *) R_alloc((long) indelBufferSize, sizeof(int));
                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:803:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        tempIntPtr = (int *) R_alloc((long) mismatchBuffer.totalSpace, sizeof(int));
                                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:804:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, mismatchBuffer.pattern, mismatchBuffer.usedSpace * sizeof(int));
                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:804:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, mismatchBuffer.pattern, mismatchBuffer.usedSpace * sizeof(int));
                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:806:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        tempIntPtr = (int *) R_alloc((long) mismatchBuffer.totalSpace, sizeof(int));
                                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:807:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, mismatchBuffer.subject, mismatchBuffer.usedSpace * sizeof(int));
                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:807:64: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, mismatchBuffer.subject, mismatchBuffer.usedSpace * sizeof(int));
                                                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:812:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthMismatch * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:812:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthMismatch * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:815:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthMismatch * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:815:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthMismatch * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:828:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        tempIntPtr = (int *) R_alloc((long) indel1Buffer.totalSpace, sizeof(int));
                                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:829:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel1Buffer.start, indel1Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:829:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel1Buffer.start, indel1Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:831:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        tempIntPtr = (int *) R_alloc((long) indel1Buffer.totalSpace, sizeof(int));
                                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:832:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel1Buffer.width, indel1Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:832:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel1Buffer.width, indel1Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:836:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:836:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:838:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:838:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align1Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:851:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        tempIntPtr = (int *) R_alloc((long) indel2Buffer.totalSpace, sizeof(int));
                                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:852:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel2Buffer.start, indel2Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:852:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel2Buffer.start, indel2Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:854:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                        tempIntPtr = (int *) R_alloc((long) indel2Buffer.totalSpace, sizeof(int));
                                                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:855:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel2Buffer.width, indel2Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:855:58: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(tempIntPtr, indel2Buffer.width, indel2Buffer.usedSpace * sizeof(int));
                                                                               ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:859:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align2Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:859:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align2Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:861:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align2Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:861:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                           align2Info.lengthIndel * sizeof(int));
                                           ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:894:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           mismatchBuffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:894:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           mismatchBuffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:905:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel1Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:905:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel1Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:907:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel1Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:907:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel1Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:932:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           mismatchBuffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:932:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           mismatchBuffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:943:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel2Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:943:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel2Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:945:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel2Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_pairwiseAlignment.c:945:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                           indel2Buffer.usedSpace * sizeof(int));
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_pairwiseAlignment.c:1026:26: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        float gapOpeningValue = REAL(gapOpening)[0];
              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:1027:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
        float gapExtensionValue = REAL(gapExtension)[0];
              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:1030:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                gapExtensionValue = NEGATIVE_INFINITY;
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:11:27: note: expanded from macro 'NEGATIVE_INFINITY'
#define NEGATIVE_INFINITY R_NegInf
                          ^˜˜˜˜˜˜˜
align_pairwiseAlignment.c:1063:54: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        alignBuffer.currMatrix = (float *) R_alloc((long) 3 * alignmentBufferSize, sizeof(float));
                                           ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_pairwiseAlignment.c:1064:54: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        alignBuffer.prevMatrix = (float *) R_alloc((long) 3 * alignmentBufferSize, sizeof(float));
                                           ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
85 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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c align_utils.c -o align_utils.o
align_utils.c:126:52: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                        memcpy(&alignedStringPtr[index], origStringPtr, *rangeWidth * sizeof(char));
                                                                        ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_utils.c:126:52: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                        memcpy(&alignedStringPtr[index], origStringPtr, *rangeWidth * sizeof(char));
                                                                        ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_utils.c:135:54: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(&alignedStringPtr[index], origStringPtr, copyElements * sizeof(char));
                                                                                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_utils.c:135:54: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                        memcpy(&alignedStringPtr[index], origStringPtr, copyElements * sizeof(char));
                                                                                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_utils.c:146:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        memcpy(&alignedStringPtr[index], origStringPtr, copyElements * sizeof(char));
                                                                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_utils.c:146:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        memcpy(&alignedStringPtr[index], origStringPtr, copyElements * sizeof(char));
                                                                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_utils.c:278:37: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        char *outputPtr = (char *) R_alloc((long) (INTEGER(maxNChar)[0] + 1), sizeof(char));
                                   ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
align_utils.c:288:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(outputPtr, patternPtr, numberOfChars * sizeof(char));
                                              ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
align_utils.c:288:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(outputPtr, patternPtr, numberOfChars * sizeof(char));
                                              ^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
align_utils.c:287:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                int numberOfChars = strlen(patternPtr);
                    ˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c find_palindromes.c -o find_palindromes.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c gtestsim.c -o gtestsim.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inject_code.c -o inject_code.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c io_utils.c -o io_utils.o
io_utils.c:24:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        res = fread(buf, 5, 1, fp);
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
io_utils.c:69:6: warning: unused variable 'ret' [-Wunused-variable]
        int ret, ztype, subtype;
            ^
io_utils.c:70:14: warning: unused variable 'buf' [-Wunused-variable]
        struct stat buf;
                    ^
io_utils.c:185:10: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                size = strlen(buf);
                     ˜ ^˜˜˜˜˜˜˜˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c letter_frequency.c -o letter_frequency.o
letter_frequency.c:389:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
                                ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:389:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
                                ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:411:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:411:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:419:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:419:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:527:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:527:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:536:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:536:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(ans_row, 0, LENGTH(ans) * sizeof(int));
                                   ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:730:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(INTEGER(ans), 0, ans_length * sizeof(int));
                                ^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:730:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(INTEGER(ans), 0, ans_length * sizeof(int));
                                ^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:837:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
                          ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:837:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
                          ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:857:24: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
  Rboolean _collapse = asLogical(collapse);
           ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
letter_frequency.c:878:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ans_mat, 0, LENGTH(ans) * sizeof(int));
                     ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:878:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ans_mat, 0, LENGTH(ans) * sizeof(int));
                     ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
letter_frequency.c:853:13: warning: unused variable 'ans_dimnames' [-Wunused-variable]
  SEXP ans, ans_dimnames;
            ^
letter_frequency.c:854:48: warning: unused variable 'x_pos' [-Wunused-variable]
  int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                               ^
letter_frequency.c:959:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ans_mat, 0, LENGTH(ans) * sizeof(int));
                     ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
letter_frequency.c:959:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ans_mat, 0, LENGTH(ans) * sizeof(int));
                     ^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
21 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c lowlevel_matching.c -o lowlevel_matching.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_BOC.c -o match_BOC.o
match_BOC.c:82:37: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
                        buf1[n1] = buf2[n1] = buf3[n1] = 255;
                                                       ˜ ^˜˜
match_BOC.c:92:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                partsum1 += buf1[n1] = c1_oc;
                                     ˜ ^˜˜˜˜
match_BOC.c:93:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                partsum2 += buf2[n1] = c2_oc;
                                     ˜ ^˜˜˜˜
match_BOC.c:94:26: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                partsum3 += buf3[n1] = c3_oc;
                                     ˜ ^˜˜˜˜
match_BOC.c:244:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                codes[i] = tmp_codes[ii];
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
match_BOC.c:316:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(Psuf4, Ssuf4, nPsuf4) != 0)
                    ˜˜˜˜˜˜               ^˜˜˜˜˜
match_BOC.c:331:3: warning: unused label 'continue0' [-Wunused-label]
                continue0: ;
                ^˜˜˜˜˜˜˜˜˜˜
match_BOC.c:268:55: warning: unused variable 'j' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                             ^
match_BOC.c:268:59: warning: unused variable 'offsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                 ^
match_BOC.c:268:68: warning: unused variable 'noffsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                          ^
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_BOC2.c -o match_BOC2.o
match_BOC2.c:211:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                codes[i] = tmp_codes[ii];
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
match_BOC2.c:273:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(Psuf4, Ssuf4, nPsuf4) != 0)
                    ˜˜˜˜˜˜               ^˜˜˜˜˜
match_BOC2.c:288:3: warning: unused label 'continue0' [-Wunused-label]
                continue0: ;
                ^˜˜˜˜˜˜˜˜˜˜
match_BOC2.c:234:55: warning: unused variable 'j' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                             ^
match_BOC2.c:234:59: warning: unused variable 'offsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                 ^
match_BOC2.c:234:68: warning: unused variable 'noffsets' [-Wunused-variable]
            nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
                                                                          ^
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_PWM.c -o match_PWM.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pattern.c -o match_pattern.o
match_pattern.c:55:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(p, s, plen) == 0)
                    ˜˜˜˜˜˜       ^˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
match_pattern_boyermoore.c:91:32: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                ppP.seq = (char *) malloc(P->length * sizeof(char));
                                          ˜˜˜^˜˜˜˜˜ ˜
match_pattern_boyermoore.c:149:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(ppP.seq + j, ppP.seq + j0, length) == 0) {
                    ˜˜˜˜˜˜                            ^˜˜˜˜˜
match_pattern_boyermoore.c:155:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(ppP.seq, ppP.seq + shift0, length) == 0)
                    ˜˜˜˜˜˜                            ^˜˜˜˜˜
match_pattern_boyermoore.c:209:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(tmp, tmp + shift, length) == 0)
                    ˜˜˜˜˜˜                   ^˜˜˜˜˜
match_pattern_boyermoore.c:228:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        malloc(256 * ppP.buflength * sizeof(int));
                               ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
match_pattern_boyermoore.c:333:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (memcmp(tmp, tmp + shift, length) == 0)
                    ˜˜˜˜˜˜                   ^˜˜˜˜˜
match_pattern_boyermoore.c:350:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        malloc(ppP.buflength * ppP.buflength * sizeof(int));
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
7 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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:15:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        P.length = strlen(P.seq);
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
match_pattern_indels.c:17:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        S.length = strlen(S.seq);
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pattern_shiftor.c -o match_pattern_shiftor.o
match_pattern_shiftor.c:251:12: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        R_alloc(PMmask_length, sizeof(ShiftOrWord_t));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pdict.c -o match_pdict.o
match_pdict.c:120:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(INTEGER(ans), 0, ans_length * sizeof(int));
                                        ^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
match_pdict.c:120:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(INTEGER(ans), 0, ans_length * sizeof(int));
                                        ^˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
match_pdict.c:440:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                sizeof(int) * tb_length);
                                            ˜ ^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
match_pdict.c:440:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                                sizeof(int) * tb_length);
                                            ˜ ^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c:82:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res += (unsigned int) (depth + 1 - d) * nleaves;
                                                              ˜ ^˜˜˜˜˜˜
match_pdict_ACtree2.c:154:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        delta = max_nn - nleaves - n2;  /* should always be >= 0 */
                              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
match_pdict_ACtree2.c:154:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        delta = max_nn - nleaves - n2;  /* should always be >= 0 */
                                       ˜ ^˜˜˜˜˜˜
match_pdict_ACtree2.c:240:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
               + *(buf->lastblock_nelt);
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
match_pdict_ACtree2.c:343:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
               + *(buf->lastblock_nelt);
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
match_pdict_ACtree2.c:724:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        return ScalarInteger(TREE_SIZE(&tree));
               ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
match_pdict_ACtree2.c:483:25: note: expanded from macro 'TREE_SIZE'
#define TREE_SIZE(tree) get_ACnodeBuf_nelt(&((tree)->nodebuf)) /* nb nodes */
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
match_pdict_ACtree2.c:1104:40: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        return *((const ACnode * const *) p1) - *((const ACnode * const *) p2);
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
match_pdict_ACtree2.c:1108:11: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        qsort(x, nelt, sizeof(ACnode *), compar_node_pointers_for_sort);
        ˜˜˜˜˜    ^˜˜˜
match_pdict_ACtree2.c:640:21: warning: unused function 'a_nice_max_nodeextbuf_nelt' [-Wunused-function]
static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                    ^
9 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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pdict_Twobit.c -o match_pdict_Twobit.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c:197:4: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        LENGTH(dups) * sizeof(int));
                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
match_pdict_utils.c:197:4: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        LENGTH(dups) * sizeof(int));
                        ^˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
match_pdict_utils.c:445:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                if (nrow > bmbuf[i].nword_per_col * NBIT_PER_BITWORD)
                           ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
match_pdict_utils.c:457:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        if (nrow > bmbuf->nword_per_col * NBIT_PER_BITWORD)
                   ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
match_pdict_utils.c:664:49: warning: unused variable 'ncol' [-Wunused-variable]
        int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                       ^
match_pdict_utils.c:726:10: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        nkey2 = nkey0 % NBIT_PER_BITWORD;
                ^˜˜˜˜ ˜
match_pdict_utils.c:722:6: warning: unused variable 'nelt' [-Wunused-variable]
        int nelt, nkey0, nkey1, nkey2, i;
            ^
match_pdict_utils.c:821:44: warning: unused variable 'subtotal_NFC' [-Wunused-variable]
        static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                                  ^
match_pdict_utils.c:820:20: warning: unused variable 'ndup' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^
match_pdict_utils.c:821:27: warning: unused variable 'total_NFC' [-Wunused-variable]
        static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                 ^
match_pdict_utils.c:820:33: warning: unused variable 'NFC' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                       ^
match_pdict_utils.c:820:26: warning: unused variable 'nloci' [-Wunused-variable]
        unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                ^
match_pdict_utils.c:275:13: warning: unused function 'match_headtail_by_loc' [-Wunused-function]
static void match_headtail_by_loc(const HeadTail *headtail,
            ^
13 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c match_reporting.c -o match_reporting.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c matchprobes.c -o matchprobes.o
matchprobes.c:73:19: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    rv->pos1 = (m - x)/sizeof(char) + 1;
                ˜˜^˜˜ ˜
matchprobes.c:91:19: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
    rv->pos1 = (m - x)/sizeof(char) + 1;
                ˜˜^˜˜ ˜
matchprobes.c:73:37: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    rv->pos1 = (m - x)/sizeof(char) + 1;
             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
matchprobes.c:75:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    rv->len  = strlen(y);
             ˜ ^˜˜˜˜˜˜˜˜
matchprobes.c:80:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  len = strlen(y);
      ˜ ^˜˜˜˜˜˜˜˜
matchprobes.c:91:37: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    rv->pos1 = (m - x)/sizeof(char) + 1;
             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c pmatchPattern.c -o pmatchPattern.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c replace_letter_at.c -o replace_letter_at.o
replace_letter_at.c:45:22: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                        if ((new_letter = byte2code[byte]) == NA_INTEGER) {
                                        ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c strutils.c -o strutils.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c translate.c -o translate.o
translate.c:63:14: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
        skipcode0 = (unsigned char) INTEGER(skipcode)[0];
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c utils.c -o utils.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"   -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c xscat.c -o xscat.o
xscat.c:106:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                *start = ans_tag_length + 1U;
                       ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
xscat.c:116:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                ans_tag_length += *width;
                               ˜˜ ^˜˜˜˜˜
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 Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSet_class.o XStringSet_io.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o utils.o xscat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Biostrings.Rcheck/Biostrings/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'setequal' from package 'base' in package 'Biostrings'
Creating a generic function for 'ls' from package 'base' in package 'Biostrings'
Creating a new generic function for 'offset' in package 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biostrings)

Biostrings.Rcheck/Biostrings-Ex.timings:

nameusersystemelapsed
AAString-class0.0160.0040.020
AMINO_ACID_CODE0.2210.0030.225
AlignedXStringSet-class0.1450.0150.159
DNAString-class0.0120.0030.014
GENETIC_CODE0.0160.0030.020
HNF4alpha0.0470.0030.049
IUPAC_CODE_MAP0.0260.0010.027
MIndex-class0.0130.0010.014
MaskedXString-class0.4290.0360.503
MultipleAlignment-class3.4700.0463.536
PDict-class13.137 0.54113.948
PairwiseAlignments-class0.6890.1130.805
PairwiseAlignments-io3.4390.4093.873
QualityScaledXStringSet-class0.0410.0110.053
RNAString-class0.0240.0140.037
XString-class0.0280.0250.052
XStringQuality-class0.1680.0360.204
XStringSet-class14.644 2.16217.002
XStringSet-comparison6.7851.5598.514
XStringSet-io14.693 1.45616.491
XStringSetList-class0.2580.0320.291
XStringViews-class0.3520.0540.406
align-utils0.1800.0540.235
chartr1.9770.1012.104
detail1.5380.0651.690
dinucleotideFrequencyTest0.0230.0110.033
findPalindromes14.192 0.11014.519
getSeq0.1160.0180.135
gregexpr20.0050.0060.011
injectHardMask0.0820.0160.099
letter0.1550.0290.186
letterFrequency3.9940.6304.695
longestConsecutive0.0030.0050.008
lowlevel-matching1.4270.3081.742
maskMotif2.8670.3033.232
match-utils0.0520.0110.063
matchLRPatterns1.1420.1081.292
matchPDict-exact530.181 11.568559.147
matchPDict-inexact 89.870 3.618100.940
matchPWM11.785 0.08212.413
matchPattern 9.370 0.35911.222
matchProbePair3.0690.0783.224
matchprobes0.5470.0330.617
misc0.0320.0100.042
needwunsQS0.0050.0110.016
nucleotideFrequency2.4550.2732.768
pairwiseAlignment1.1590.3321.523
phiX174Phage1.1780.2141.396
pid0.4660.1240.594
replaceLetterAt1.5930.6242.245
reverseComplement4.8910.8375.839
stringDist38.284 0.22442.775
substitution_matrices0.7570.2190.987
toComplex0.0070.0100.017
translate2.0460.1022.279
trimLRPatterns0.1570.0190.186
xscat3.1950.5233.857
yeastSEQCHR10.0080.0060.014