>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Biostrings.buildbin-libdir Biostrings_2.28.0.tar.gz'
>>>>>>>
* 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 -g -O2 -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 -g -O2 -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 -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" -fPIC -mtune=native -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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:234:59: 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;
^
match_BOC2.c:234:55: warning: unused variable 'j' [-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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Biostrings.buildbin-libdir/Biostrings/libs//Biostrings.so"