>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.20.1.tar.gz'
>>>>>>>
* installing *source* package 'rtracklayer' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -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 -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_rtracklayer.c -o R_init_rtracklayer.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c bigWig.c -o bigWig.o
bigWig.c:22:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
item->end = start[i] + width[i] - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:23:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
item->start = start[i] - 1;
˜ ˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:24:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
item->val = score[i];
˜ ^˜˜˜˜˜˜˜
bigWig.c:35:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
lmAllocArray(lm, packed, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ucsc/localmem.h:45:69: note: expanded from macro 'lmAllocArray'
#define lmAllocArray(lm, pt, size) (pt = lmAlloc(lm, sizeof(*pt) * (size)))
^
bigWig.c:39:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
packed[i].start = start[i] - 1;
˜ ˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:40:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
packed[i].val = score[i];
˜ ^˜˜˜˜˜˜˜
bigWig.c:49:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
lmAllocArray(lm, packed, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
./ucsc/localmem.h:45:69: note: expanded from macro 'lmAllocArray'
#define lmAllocArray(lm, pt, size) (pt = lmAlloc(lm, sizeof(*pt) * (size)))
^
bigWig.c:53:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
packed[i].val = score[i];
˜ ^˜˜˜˜˜˜˜
bigWig.c:65:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
section->start = start[0] - 1;
˜ ˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:66:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
section->end = start[len-1] + width[len-1] - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:68:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
section->itemSpan = width[0];
˜ ^˜˜˜˜˜˜˜
bigWig.c:71:44: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
section->itemStep = len > 1 ? start[1] - start[0] : 0;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
bigWig.c:77:24: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
section->itemCount = len;
˜ ^˜˜
bigWig.c:181:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER(seqlengths)[i] = chrom->size;
˜ ˜˜˜˜˜˜˜^˜˜˜
bigWig.c:199:22: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
bool returnScore = asLogical(r_return_score);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical Rf_asLogical
^
bigWig.c:218:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
start[j] - 1, start[j] - 1 + width[j], lm);
˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:218:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
start[j] - 1, start[j] - 1 + width[j], lm);
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
bigWig.c:233:43: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER(ans_start)[j] = hits->start + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:234:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER(ans_width)[j] = hits->end - hits->start;
˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
bigWig.c:281:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
bool success = bigWigSummaryArray(file, chrom, start[i] - 1,
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bigWig.c:281:61: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bool success = bigWigSummaryArray(file, chrom, start[i] - 1,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜
bigWig.c:282:52: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
start[i] - 1 + width[i], type, size,
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c chain_io.c -o chain_io.o
chain_io.c:82:13: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
trc = strcmp("+", header[4]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chain_io.c:83:13: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
qrc = strcmp("+", header[9]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
chain_io.c:66:42: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int name_size = strlen(header[2])+1;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c twoBit.c -o twoBit.o
twoBit.c:22:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(twoBit->maskStarts, mask_count);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
./ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
twoBit.c:23:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(twoBit->maskSizes, mask_count);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
./ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
twoBit.c:26:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
twoBit->maskStarts[i] = mask_start[i] - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
twoBit.c:27:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
twoBit->maskSizes[i] = mask_width[i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
twoBit.c:13:46: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
struct dnaSeq *seq = newDnaSeq((DNA *)dna, strlen(dna),
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
twoBit.c:109:37: warning: passing 'Rbyte *' (aka 'unsigned char *') to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
RAW(r_seq), total_width,
^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include/IRanges_interface.h:342:8: note: passing argument to parameter 'dest' here
char *dest,
^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c handlers.c -o handlers.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c utils.c -o utils.o
utils.c:4:8: warning: unused variable 'ans' [-Wunused-variable]
SEXP ans;
^
utils.c:21:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int src_len = strlen(src);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
ucsc/bPlusTree.c:138:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:139:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, val, bpt->valSize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:148:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:156:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:186:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:187:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, valBuf, bpt->valSize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:188:33: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
callback(context, keyBuf, bpt->keySize, valBuf, bpt->valSize);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:188:55: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
callback(context, keyBuf, bpt->keySize, valBuf, bpt->valSize);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:197:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
udcMustRead(bpt->udc, keyBuf, bpt->keySize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bPlusTree.c:222:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
memset(keyBuf+keySize, 0, bpt->keySize - keySize);
˜ ^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
ucsc/bPlusTree.c:222:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
memset(keyBuf+keySize, 0, bpt->keySize - keySize);
˜ ^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
ucsc/bPlusTree.c:240:1: warning: void function 'bptFileTraverse' should not return void expression [-Wpedantic]
return rTraverse(bpt, bpt->rootOffset, context, callback);
^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:287:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int slotSizePer = xToY(blockSize, level); // Number of items per slot in node
˜˜˜˜ ^˜˜˜˜
ucsc/bPlusTree.c:292:45: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
int bytesInIndexBlock = (bptBlockHeaderSize + blockSize * (keySize+sizeof(bits64)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:293:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int bytesInLeafBlock = (bptBlockHeaderSize + blockSize * (keySize+valSize));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:294:46: warning: operand of ? changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 bytesInNextLevelBlock = (level == 1 ? bytesInLeafBlock : bytesInIndexBlock);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:294:65: warning: operand of ? changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 bytesInNextLevelBlock = (level == 1 ? bytesInLeafBlock : bytesInIndexBlock);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:295:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 levelSize = nodeCount * bytesInIndexBlock;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:308:56: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
bits16 countOne = (itemCount - i + slotSizePer - 1)/slotSizePer;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:335:28: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
int slotSize = keySize + sizeof(bits64);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:339:8: warning: implicit conversion loses integer precision: 'unsigned long long' to 'unsigned int' [-Wshorten-64-to-32]
return endLevel;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bPlusTree.c:362:20: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
countOne = countLeft;
˜ ^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:379:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int slotSize = keySize + valSize;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:402:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
bits64 indexOffset = ftell(f);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bPlusTree.c:405:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int levels = bptCountLevels(blockSize, itemCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:409:45: warning: implicit conversion loses integer precision: 'unsigned int' to 'unsigned short' [-Wconversion]
bits32 endLevelOffset = writeIndexLevel(blockSize, itemArray, itemSize, itemCount, indexOffset,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:411:19: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
indexOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bPlusTree.c:417:16: warning: implicit conversion loses integer precision: 'unsigned int' to 'unsigned short' [-Wconversion]
writeLeafLevel(blockSize, itemArray, itemSize, itemCount,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:405:40: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int levels = bptCountLevels(blockSize, itemCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:409:77: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
bits32 endLevelOffset = writeIndexLevel(blockSize, itemArray, itemSize, itemCount, indexOffset,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:409:88: warning: implicit conversion loses integer precision: 'unsigned long long' to 'unsigned int' [-Wshorten-64-to-32]
bits32 endLevelOffset = writeIndexLevel(blockSize, itemArray, itemSize, itemCount, indexOffset,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bPlusTree.c:417:48: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
writeLeafLevel(blockSize, itemArray, itemSize, itemCount,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
32 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c:30:33: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int diff = desiredReduction - level->reductionLevel;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:30:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int diff = desiredReduction - level->reductionLevel;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ucsc/bbiRead.c:59:15: warning: implicit conversion changes signedness: 'unsigned long' to 'off_t' (aka 'long long') [-Wsign-conversion]
mustLseek(fd, -sizeof(magic), SEEK_END);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:166:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:216:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:337:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
struct fileOffsetSize *blockList = cirTreeFindOverlappingBlocks(ctf, chromId, start, end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiRead.c:391:21: warning: operand of ? changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int s = max(dSum->start, start);
˜ ˜˜˜˜˜˜^˜˜˜˜
ucsc/common.h:1159:33: note: expanded from macro 'max'
#define max(a,b) ( (a) > (b) ? (a) : (b) )
^
ucsc/bbiRead.c:391:28: warning: operand of ? changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int s = max(dSum->start, start);
˜ ^˜˜˜˜
ucsc/common.h:1159:39: note: expanded from macro 'max'
#define max(a,b) ( (a) > (b) ? (a) : (b) )
^
ucsc/bbiRead.c:392:21: warning: operand of ? changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int e = min(dSum->end, end);
˜ ˜˜˜˜˜˜^˜˜
ucsc/common.h:1154:33: note: expanded from macro 'min'
#define min(a,b) ( (a) < (b) ? (a) : (b) )
^
ucsc/bbiRead.c:392:26: warning: operand of ? changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int e = min(dSum->end, end);
˜ ^˜˜
ucsc/common.h:1154:39: note: expanded from macro 'min'
#define min(a,b) ( (a) < (b) ? (a) : (b) )
^
ucsc/bbiRead.c:356:33: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
udcMustRead(udc, mergedBuf, mergedSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:367:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int uncSize = zUncompress(blockBuf, block->size, uncompressBuf, bbi->uncompressBufSize);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:377:27: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int blockSize = blockEnd - blockPt;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:428:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:428:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiRead.c:428:59: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜
ucsc/bbiRead.c:428:71: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜
ucsc/bbiRead.c:459:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return idSize.chromId;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜
ucsc/bbiRead.c:457:40: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize)))
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:482:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
baseEnd = start + (bits64)baseCount*(i+1)/summarySize;
˜ ˜^˜
ucsc/bbiRead.c:482:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
baseEnd = start + (bits64)baseCount*(i+1)/summarySize;
˜^˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:482:18: warning: implicit conversion loses integer precision: 'unsigned long long' to 'unsigned int' [-Wshorten-64-to-32]
baseEnd = start + (bits64)baseCount*(i+1)/summarySize;
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:516:34: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, interval->start, interval->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:516:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, interval->start, interval->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiRead.c:516:64: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, interval->start, interval->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
ucsc/bbiRead.c:516:81: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(baseStart, baseEnd, interval->start, interval->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/bbiRead.c:519:39: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int intervalSize = interval->end - interval->start;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:531:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
el->validCount = round(validCount);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1147:19: note: expanded from macro 'round'
#define round(a) ((int)((a)+0.5))
^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:537:8: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return round(validCount);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1147:19: note: expanded from macro 'round'
#define round(a) ((int)((a)+0.5))
^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:559:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
baseEnd = start + (bits64)baseCount*(i+1)/summarySize;
˜ ˜^˜
ucsc/bbiRead.c:559:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
baseEnd = start + (bits64)baseCount*(i+1)/summarySize;
˜^˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:560:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int end1 = baseEnd;
˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiRead.c:562:22: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
end1 = baseStart+1;
˜ ˜˜˜˜˜˜˜˜˜^˜
ucsc/bbiRead.c:568:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (bbiIntervalSlice(bbi, baseStart, end1, interval, &summary[i]))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/bbiRead.c:559:18: warning: implicit conversion loses integer precision: 'unsigned long long' to 'unsigned int' [-Wshorten-64-to-32]
baseEnd = start + (bits64)baseCount*(i+1)/summarySize;
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:590:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
bzero(summary, summarySize * sizeof(summary[0]));
^˜˜˜˜˜˜˜˜˜˜ ˜
ucsc/bbiRead.c:595:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int fullReduction = (baseSize/summarySize);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:595:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int fullReduction = (baseSize/summarySize);
˜^˜˜˜˜˜˜˜˜˜˜
ucsc/bbiRead.c:619:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(elements, summarySize);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
39 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
ucsc/bbiWrite.c:52:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(chromInfoArray, chromCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/bbiWrite.c:67:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(chromInfoArray, chromCount, sizeof(chromInfoArray[0]), bbiChromInfoCmp);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:71:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:71:83: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:72:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bbiChromInfoKey, maxChromNameSize, bbiChromInfoVal,
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:58:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(chromName);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:92:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
hashAddInt(hash, row[0], sqlUnsigned(row[1]));
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:170:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
totalBases += (end - start);
˜˜ ˜˜˜˜^˜˜˜˜˜˜
ucsc/bbiWrite.c:186:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
usage->size = chromSize;
˜ ^˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:221:57: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int countOne = (usage->itemCount + itemsPerSlot - 1)/itemsPerSlot;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:221:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int countOne = (usage->itemCount + itemsPerSlot - 1)/itemsPerSlot;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:221:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int countOne = (usage->itemCount + itemsPerSlot - 1)/itemsPerSlot;
˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:246:59: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (sum == NULL || sum->chromId != chromId || sum->end + reduction <= start)
˜ ^˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:250:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
newSum->end = newSum->start + reduction;
˜ ^˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:253:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
newSum->minVal = minVal;
˜ ^˜˜˜˜˜
ucsc/bbiWrite.c:254:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
newSum->maxVal = maxVal;
˜ ^˜˜˜˜˜
ucsc/bbiWrite.c:260:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(start, end, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/bbiWrite.c:260:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(start, end, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ucsc/bbiWrite.c:260:54: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(start, end, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜
ucsc/bbiWrite.c:260:66: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int overlap = rangeIntersection(start, end, sum->start, sum->end);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜
ucsc/bbiWrite.c:266:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int itemSize = end - start;
˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
ucsc/bbiWrite.c:272:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sum->minVal = minVal;
˜ ^˜˜˜˜˜
ucsc/bbiWrite.c:274:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sum->maxVal = maxVal;
˜ ^˜˜˜˜˜
ucsc/bbiWrite.c:279:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
start += overlap;
˜˜ ^˜˜˜˜˜˜
ucsc/bbiWrite.c:288:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int size = end-start;
˜˜˜˜ ˜˜˜^˜˜˜˜˜
ucsc/bbiWrite.c:291:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bbiAddToSummary(chromId, chromSize, start, end, size, val, val, sum, sumSquares, reduction, pOutList);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/bbiWrite.c:342:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bits32 i, count = slCount(summaryList);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:350:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int uncBufSize = itemSize * itemsPerSlot;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:350:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int uncBufSize = itemSize * itemsPerSlot;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:352:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compBufSize = zCompBufSize(uncBufSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:362:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
itemsInSlot = itemsPerSlot;
˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:365:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
bits64 filePos = ftell(f);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:384:56: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compSize = zCompress(uncBuf, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:385:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, compBuf, compSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:389:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
bits64 indexOffset = ftell(f);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:391:5: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
blockSize, itemsPerSlot, NULL, bbiSummaryFetchKey, bbiSummaryFetchOffset,
^˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:391:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
blockSize, itemsPerSlot, NULL, bbiSummaryFetchKey, bbiSummaryFetchOffset,
^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:352:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compBufSize = zCompBufSize(uncBufSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:383:30: warning: implicit conversion loses integer precision: 'long' to 'unsigned int' [-Wshorten-64-to-32]
bits32 uncSize = writePt - uncBuf;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:384:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compSize = zCompress(uncBuf, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:402:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bits32 i, count = slCount(summaryList);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:410:27: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
summary->fileOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:420:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
bits64 indexOffset = ftell(f);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:422:5: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
blockSize, itemsPerSlot, NULL, bbiSummaryFetchKey, bbiSummaryFetchOffset,
^˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:422:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
blockSize, itemsPerSlot, NULL, bbiSummaryFetchKey, bbiSummaryFetchOffset,
^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:458:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(stream->array, allocCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/bbiWrite.c:470:35: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
int uncSize = stream->elCount * sizeof(stream->array[0]);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:470:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int uncSize = stream->elCount * sizeof(stream->array[0]);
˜˜˜˜˜˜˜˜^˜˜˜˜˜˜ ˜
ucsc/bbiWrite.c:473:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compBufSize = zCompBufSize(uncSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiWrite.c:475:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compSize = zCompress(stream->array, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiWrite.c:475:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compSize = zCompress(stream->array, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:476:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(stream->f, compBuf, compSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bbiWrite.c:480:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(stream->f, stream->array, uncSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bbiWrite.c:473:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compBufSize = zCompBufSize(uncSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:475:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compSize = zCompress(stream->array, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:531:18: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
bounds->offset = ftell(stream->f);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:542:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
|| twiceReduced->start + doubleReductionSize < sum->end)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bbiWrite.c:566:89: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if (newSum == NULL || newSum->chromId != sum->chromId || sum->end > newSum->start + reduction)
˜ ^˜˜˜˜˜˜˜˜
58 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
ucsc/bwgCreate.c:76:23: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
section->fileOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:129:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t maxCompSize = zCompBufSize(bufSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bwgCreate.c:131:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compSize = zCompress(buf, bufSize, compBuf, maxCompSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bwgCreate.c:132:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, compBuf, compSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:135:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, buf, bufSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/bwgCreate.c:131:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compSize = zCompress(buf, bufSize, compBuf, maxCompSize);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:211:17: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
item->val = lineFileNeedDouble(lf, words, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:244:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
sectionStart += sectionSize * step;
^˜˜˜˜˜˜˜˜˜˜ ˜
ucsc/bwgCreate.c:249:26: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
section->itemCount = sectionSize;
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:253:63: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
section->items.fixedStepPacked = lmAllocArray(lm, packed, sectionSize);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/localmem.h:45:69: note: expanded from macro 'lmAllocArray'
#define lmAllocArray(lm, pt, size) (pt = lmAlloc(lm, sizeof(*pt) * (size)))
^
ucsc/bwgCreate.c:295:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
item->start = start - 1;
˜ ˜˜˜˜˜˜^˜˜
ucsc/bwgCreate.c:296:17: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
item->val = lineFileNeedDouble(lf, words, 1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:338:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
p = lmAllocArray(lm, packed, sectionSize);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/localmem.h:45:69: note: expanded from macro 'lmAllocArray'
#define lmAllocArray(lm, pt, size) (pt = lmAlloc(lm, sizeof(*pt) * (size)))
^
ucsc/bwgCreate.c:357:26: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
section->itemCount = sectionSize;
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:407:9: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
span = parseUnsignedVal(lf, var, val);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:422:37: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bits32 chromSize = (chromSizeHash ? hashIntVal(chromSizeHash, chrom) : BIGNUM);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:437:9: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
span = step;
˜ ^˜˜˜
ucsc/bwgCreate.c:439:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chrom, chromSize, span, start-1, step, pSectionList);
^˜˜˜
ucsc/bwgCreate.c:450:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
chrom, chromSize, span, pSectionList);
^˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:450:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chrom, chromSize, span, pSectionList);
^˜˜˜
ucsc/bwgCreate.c:504:33: warning: operand of ? changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chrom->size = (chromSizeHash ? hashIntVal(chromSizeHash, chromName) : BIGNUM);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:510:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
item->start = lineFileNeedNum(lf, words, 1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:511:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
item->end = lineFileNeedNum(lf, words, 2);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:512:17: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
item->val = lineFileNeedDouble(lf, words, 3);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:575:23: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
section->itemCount = sectionSize;
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:609:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
section->chromId = chromCount-1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜
ucsc/bwgCreate.c:615:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(chromArray, chromCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/bwgCreate.c:620:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chromArray[i].id = i;
˜ ^
ucsc/bwgCreate.c:621:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
chromArray[i].size = hashIntVal(chromSizeHash, uniq->val);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:605:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(chromName);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:651:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int size = item->end - item->start;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:670:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
sectionRes = smallestGap;
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:672:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
sectionRes = section->itemSpan;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:677:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
sectionRes = section->itemStep;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:684:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
totalRes += sectionRes;
˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:687:35: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
return (totalRes + sectionCount/2)/sectionCount;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:724:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
total += bwgSectionSize(section);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:759:22: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int start = section->start;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
ucsc/bwgCreate.c:763:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bbiAddRangeToSummary(section->chromId, chromSize, start, start + section->itemSpan, items->val,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/bwgCreate.c:763:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bbiAddRangeToSummary(section->chromId, chromSize, start, start + section->itemSpan, items->val,
^˜˜˜˜ ˜
ucsc/bwgCreate.c:805:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 sectionCount = slCount(sectionList);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:855:59: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int nextReduction = 1.1 * initialReduction * summarySize / maxReducedSize;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:867:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
reductionAmounts[0] = initialReduction;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:870:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 reduction = initialReduction;
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:894:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
chromTreeOffsetPos = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:896:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
dataOffsetPos = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:898:18: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
indexOffsetPos = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:903:25: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
totalSummaryOffsetPos = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:905:24: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
uncompressBufSizePos = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:915:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
reductionDataOffsetPos[i] = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:923:22: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
totalSummaryOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:927:19: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
chromTreeOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:929:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:929:83: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:930:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bbiChromInfoKey, maxChromNameSize, bbiChromInfoVal,
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:935:14: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
dataOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:940:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bits32 uncSizeOne = bwgSectionWrite(section, doCompress, f);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:947:15: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
indexOffset = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:953:5: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
blockSize, 1, NULL, bwgSectionFetchKey, bwgSectionFetchOffset,
^˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:961:31: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
reductionDataOffsets[i] = ftell(f);
˜ ^˜˜˜˜˜˜˜
ucsc/bwgCreate.c:963:128: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
verbose(3, "wrote %d of data, %d of index on level %d\n", (int)(reductionIndexOffsets[i] - reductionDataOffsets[i]), (int)(ftell(f) - reductionIndexOffsets[i]), i);
^˜˜˜˜˜˜˜ ˜
ucsc/bwgCreate.c:984:14: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, totalSummaryOffset, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:991:10: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, dataOffsetPos, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:993:10: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, indexOffsetPos, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:995:10: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, chromTreeOffsetPos, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:997:10: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, totalSummaryOffsetPos, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:1002:42: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
int maxZoomUncompSize = itemsPerSlot * sizeof(struct bbiSummaryOnDisk);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:1002:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int maxZoomUncompSize = itemsPerSlot * sizeof(struct bbiSummaryOnDisk);
^˜˜˜˜˜˜˜˜˜˜˜ ˜
ucsc/bwgCreate.c:1004:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
uncompressBufSize = maxZoomUncompSize;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:1005:14: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, uncompressBufSizePos, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:1012:14: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, reductionDataOffsetPos[i], SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:877:6: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
reduction);
^˜˜˜˜˜˜˜˜
ucsc/bwgCreate.c:882:35: warning: implicit conversion loses integer precision: 'unsigned long long' to 'unsigned int' [-Wshorten-64-to-32]
reductionAmounts[summaryCount] = reduction;
˜ ^˜˜˜˜˜˜˜˜
73 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c:63:14: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
head->type = *pt++;
˜ ^˜˜˜˜
ucsc/bwgQuery.c:64:18: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
head->reserved = *pt++;
˜ ^˜˜˜˜
ucsc/bwgQuery.c:89:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, end) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:89:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, end) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bwgQuery.c:89:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, end) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/bwgQuery.c:89:57: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, end) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ucsc/bwgQuery.c:106:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:106:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bwgQuery.c:106:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/bwgQuery.c:106:62: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:123:28: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:123:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/bwgQuery.c:123:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/bwgQuery.c:123:62: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (rangeIntersection(rangeStart, rangeEnd, start, start+head.itemSpan) > 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:179:33: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
udcMustRead(udc, mergedBuf, mergedSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:190:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int uncSize = zUncompress(blockBuf, block->size, uncompressBuf, bwf->uncompressBufSize);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:311:33: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
udcMustRead(udc, mergedBuf, mergedSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:322:20: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int uncSize = zUncompress(blockBuf, block->size, uncompressBuf, bwf->uncompressBufSize);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/bwgQuery.c:381:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bigWigSummaryArray(bwf, chrom, start, end, summaryType, 1, &arrayOfOne);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/bwgQuery.c:381:39: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bigWigSummaryArray(bwf, chrom, start, end, summaryType, 1, &arrayOfOne);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
20 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c:62:23: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
bits16 countOne = slCount(tree->children);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:75:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
offset += childNodeSize;
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:97:18: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
rWriteIndexLevel(blockSize, childNodeSize, tree, 0, level, offsetOfFirstChild, f);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/cirTree.c:109:23: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
bits16 countOne = slCount(tree->children);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:171:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
for (i=0; i<itemCount; i += itemsPerSlot)
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:187:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
char *startItem = items + itemSize * i;
^˜˜˜˜˜˜˜ ˜
ucsc/cirTree.c:209:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
void *item = items + itemSize*(i+j);
^˜˜˜˜˜˜˜˜
ucsc/cirTree.c:209:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
void *item = items + itemSize*(i+j);
˜^
ucsc/cirTree.c:176:28: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int oneSize = itemCount-i;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
ucsc/cirTree.c:308:17: warning: implicit conversion changes signedness: 'long' to 'unsigned long long' [-Wsign-conversion]
bits64 offset = ftell(f);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/cirTree.c:309:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 iNodeSize = indexNodeSize(blockSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:310:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 lNodeSize = leafNodeSize(blockSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:314:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
offset += levelSizes[i] * iNodeSize;
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
ucsc/cirTree.c:327:32: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
writeIndexLevel(blockSize, childNodeSize, tree,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:350:51: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
struct rTree *tree = rTreeFromChromRangeArray(lm, blockSize, itemsPerSlot,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/cirTree.c:350:62: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
struct rTree *tree = rTreeFromChromRangeArray(lm, blockSize, itemsPerSlot,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:365:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
writeTreeToOpenFile(tree, blockSize, levelCount, f);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/cirTree.c:475:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return cmpTwoBits32(qChrom, qStart, rEndChrom, rEndBase) > 0 &&
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
ucsc/cirTree.c:475:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return cmpTwoBits32(qChrom, qStart, rEndChrom, rEndBase) > 0 &&
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
ucsc/cirTree.c:475:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return cmpTwoBits32(qChrom, qStart, rEndChrom, rEndBase) > 0 &&
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/cirTree.c:475:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
return cmpTwoBits32(qChrom, qStart, rEndChrom, rEndBase) > 0 &&
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/cirTree.c:476:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cmpTwoBits32(qChrom, qEnd, rStartChrom, rStartBase) < 0;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
ucsc/cirTree.c:476:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cmpTwoBits32(qChrom, qEnd, rStartChrom, rStartBase) < 0;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/cirTree.c:476:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cmpTwoBits32(qChrom, qEnd, rStartChrom, rStartBase) < 0;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:476:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
cmpTwoBits32(qChrom, qEnd, rStartChrom, rStartBase) < 0;
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:510:22: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/cirTree.c:510:31: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/cirTree.c:510:38: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ucsc/cirTree.c:510:43: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:510:57: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/cirTree.c:510:68: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:510:80: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx, startBase, endChromIx, endBase))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/cirTree.c:538:22: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx[i], startBase[i],
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/cirTree.c:538:31: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx[i], startBase[i],
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/cirTree.c:538:38: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx[i], startBase[i],
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ucsc/cirTree.c:538:43: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx[i], startBase[i],
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:538:60: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if (cirTreeOverlaps(chromIx, start, end, startChromIx[i], startBase[i],
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:539:3: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
endChromIx[i], endBase[i]))
^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/cirTree.c:539:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
endChromIx[i], endBase[i]))
^˜˜˜˜˜˜˜˜˜
39 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/common.c -o ucsc/common.o
ucsc/common.c:26:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *d = needMem(copySize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜
ucsc/common.c:36:27: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return cloneStringZExt(s, strlen(s), size);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/common.c:45:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
size = strlen(s);
˜ ^˜˜˜˜˜˜˜˜
ucsc/common.c:61:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *newBuf = needLargeMem(len+1);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^˜
ucsc/common.c:59:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int aLen = strlen(a), bLen = strlen(b);
˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/common.c:59:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int aLen = strlen(a), bLen = strlen(b);
˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/common.c:329:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
array = needLargeMem(count * sizeof(*array));
^˜˜˜˜ ˜
ucsc/common.c:332:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(array, count, sizeof(array[0]), compare);
˜˜˜˜˜ ^˜˜˜˜
ucsc/common.c:445:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(array, count, sizeof(array[0]), doubleCmp);
˜˜˜˜˜ ^˜˜˜˜
ucsc/common.c:513:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(array,count);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/common.c:530:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(array,count);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/common.c:555:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(array, count, sizeof(array[0]), intCmp);
˜˜˜˜˜ ^˜˜˜˜
ucsc/common.c:569:46: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
median = (array[count] + array[count-1]) * 0.5;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
ucsc/common.c:582:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
sn = needMem(sizeof(*sn)+len);
˜^˜˜
ucsc/common.c:581:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(name);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:596:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
struct slName *sn = needMem(sizeof(*sn) + size);
˜ ^˜˜˜
ucsc/common.c:744:29: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
el = slNameNewN(s, e-s);
˜˜˜˜˜˜˜˜˜˜ ˜^˜
ucsc/common.c:823:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(s, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/common.c:1122:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *str = needMem(count+5); // A bit of slop
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜
ucsc/common.c:1176:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *str = needMem(count+5); // A bit of slop
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜
ucsc/common.c:1256:26: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return ((char *)(a->val) - (char *)(b->val)); // cast works and val is 0 vased integer
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1292:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
c1 = toupper(*s1++);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1293:10: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
c2 = toupper(*s2++);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1339:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(firstWord);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1398:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (memcmp(needle, pos, nSize) == 0)
˜˜˜˜˜˜ ^˜˜˜˜
ucsc/common.c:1394:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nSize = strlen(needle);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1417:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pos = cloneMem(pos, len + 1);
˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜
ucsc/common.c:1416:17: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
len = p - pos;
˜ ˜˜^˜˜˜˜
ucsc/common.c:1429:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
sLen = strlen(string);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1430:8: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
eLen = strlen(end);
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1479:54: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (*haystack++ == c && memcmp(needle, haystack, nLen) == 0)
˜˜˜˜˜˜ ^˜˜˜
ucsc/common.c:1492:12: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s[i] = toupper(s[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1500:12: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
s[i] = tolower(s[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1512:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
c = tolower(c);
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/common.c:1514:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
c = toupper(c);
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/common.c:1528:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
*ss++ = toupper(c);
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/common.c:1554:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1159:21: note: expanded from macro 'max'
#define max(a,b) ( (a) > (b) ? (a) : (b) )
^
ucsc/common.c:1554:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1159:33: note: expanded from macro 'max'
#define max(a,b) ( (a) > (b) ? (a) : (b) )
^
ucsc/common.c:1555:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
result = needMem(strLen + 1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:1541:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int oldLen = strlen(old);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1542:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int newLen = strlen(new);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1554:29: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1159:33: note: expanded from macro 'max'
#define max(a,b) ( (a) > (b) ? (a) : (b) )
^
ucsc/common.c:1554:63: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
strLen = max(strlen(string) + (numTimes * (newLen - oldLen)), strlen(string));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1159:39: note: expanded from macro 'max'
#define max(a,b) ( (a) > (b) ? (a) : (b) )
^
ucsc/common.c:1561:18: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
strLen = ptr - string;
˜ ˜˜˜˜^˜˜˜˜˜˜˜
ucsc/common.c:1586:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if((strlen(string)+(count*(strlen(newStr) - strlen(oldStr))))>=sz)
^˜˜˜˜˜
ucsc/common.c:1604:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
*ss++ = tolower(c);
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/common.c:1663:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int stripSize = strlen(strip);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:1773:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int diff = memcmp(a,b,aNonNum);
˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/common.c:1910:17: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((*in == '"'))
˜˜˜˜^˜˜˜˜˜
ucsc/common.c:1910:17: note: remove extraneous parentheses around the comparison to silence this warning
if((*in == '"'))
˜ ^ ˜
ucsc/common.c:1910:17: note: use '=' to turn this equality comparison into an assignment
if((*in == '"'))
^˜
=
ucsc/common.c:2044:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(s);
˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/common.c:2155:54: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return cloneStringZ(startFirstWord, endFirstWord - startFirstWord);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:2272:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *new = needMem(size + 2); // Null terminated by 2
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜
ucsc/common.c:2400:8: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
bLen = len;
˜ ^˜˜
ucsc/common.c:2402:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, s, len);
˜˜˜˜˜˜˜˜˜ ^˜˜
ucsc/common.c:2393:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(s);
˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/common.c:2416:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = needMem(len+1);
˜˜˜˜˜˜˜ ˜˜˜^˜
ucsc/common.c:2418:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustRead(f, s, len);
˜˜˜˜˜˜˜˜ ^˜˜
ucsc/common.c:2441:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustRead(f, buf, len);
˜˜˜˜˜˜˜˜ ^˜˜
ucsc/common.c:2564:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ret = needMem(sizeof(char)*size);
˜^˜˜˜
ucsc/common.c:2563:42: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int size = strlen(head) + strlen(suffix) +1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ucsc/common.c:2765:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2766:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2767:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2768:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2769:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2770:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2771:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2772:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^ ˜
ucsc/common.c:2763:22: note: array 'bytes' declared here
union {bits64 whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2899:14: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[0] = u.bytes[7];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2900:14: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[1] = u.bytes[6];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2901:14: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[2] = u.bytes[5];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2902:14: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[3] = u.bytes[4];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2903:1: warning: array index 4 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[4] = u.bytes[3];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2904:1: warning: array index 5 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[5] = u.bytes[2];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2905:1: warning: array index 6 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[6] = u.bytes[1];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:2906:1: warning: array index 7 is past the end of the array (which contains 4 elements) [-Warray-bounds]
v.bytes[7] = u.bytes[0];
^ ˜
ucsc/common.c:2897:22: note: array 'bytes' declared here
union {double whole; UBYTE bytes[4];} u,v;
^
ucsc/common.h:106:15: note: expanded from macro 'UBYTE'
#define UBYTE unsigned char /* Wants to be unsigned 8 bits. */
^
ucsc/common.c:3002:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char* buf = needMem(bufCapacity);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:3013:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
buf = realloc(buf, bufCapacity);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:3019:22: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
buf[bufSize++] = ch;
˜ ^˜
ucsc/common.c:3077:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
haystackCopy = (char*) needMem(haystackLen + 1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/common.c:3078:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
needleCopy = (char*) needMem(needleLen + 1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/common.c:3082:27: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
haystackCopy[index] = tolower(haystack[index]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:3088:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
needleCopy[index] = tolower(needle[index]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:3074:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
haystackLen = strlen(haystack);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:3075:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
needleLen = strlen(needle);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.c:3276:39: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return cloneStringZ(s,skipToNumeric(s)-s);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
86 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/dnaseq.c -o ucsc/dnaseq.o
ucsc/dnaseq.c:34:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
seq->dna = needHugeMem(seq->size+1);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
ucsc/dnaseq.c:98:40: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
if ((inSize == 0) || (inSize > (inSeq->size - offset)))
˜˜˜˜˜˜˜^˜˜˜ ˜
ucsc/dnaseq.c:99:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
inSize = inSeq->size - offset;
˜˜˜˜˜˜˜^˜˜˜ ˜
ucsc/dnaseq.c:100:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
lastCodon = offset + inSize - 3;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/dnaseq.c:104:8: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
for (i=offset; i <= lastCodon; i += 3)
˜^˜˜˜˜˜
ucsc/dnaseq.c:167:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int sizeLog2 = digitsBaseTwo(size);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c:285:5: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
c = toupper(c);
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/dnautil.c:301:27: warning: implicit conversion loses integer precision: 'int' to 'Codon' (aka 'char') [-Wconversion]
return ((v1<<4) + (v2<<2) + v3);
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
ucsc/dnautil.c:320:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
dnaSize = strlen(dna);
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/dnautil.c:474:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*pStart = size - *pEnd;
^˜˜˜ ˜
ucsc/dnautil.c:475:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*pEnd = size - temp;
^˜˜˜ ˜
ucsc/dnautil.c:670:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
result += ntValNoN[(int)dna[i]];
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/dnautil.c:685:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
out += bVal;
˜˜ ^˜˜˜
ucsc/dnautil.c:855:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, letters, lineSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/dnautil.c:1103:12: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
lowc = tolower(c);
˜ ^˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/errabort.c -o ucsc/errabort.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/hash.c -o ucsc/hash.o
ucsc/hash.c:51:29: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
result += (result<<3) + c;
˜ ^
ucsc/hash.c:125:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int hashVal = el->hashVal & hash->mask;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/hash.c:128:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
el->name = lmAlloc(hash->lm, nameSize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜
ucsc/hash.c:140:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
hashResize(hash, digitsBaseTwo(hash->size));
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜
ucsc/hash.c:152:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return hashAddN(hash, name, strlen(name), val);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/hash.c:368:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
hash->mask = hash->size-1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜
ucsc/hash.c:369:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(hash->table, hash->size);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/hash.c:386:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
hash->mask = hash->size-1;
˜ ˜˜˜˜˜˜˜˜˜˜^˜
ucsc/hash.c:388:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(hash->table, hash->size);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/hash.c:397:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int hashVal = hel->hashVal & hash->mask;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:108:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
result=needMem(numbytes+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜
ucsc/linefile.c:109:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if ((bytesread=read(fd,result,numbytes)) < numbytes)
˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/linefile.c:109:20: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
if ((bytesread=read(fd,result,numbytes)) < numbytes)
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/linefile.c:163:69: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pl = pipelineOpenMem1(getDecompressor(fileName), pipelineRead, mem, size, STDERR_FILENO);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/linefile.c:180:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
lf->buf = needMem(lf->bufSize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜
ucsc/linefile.c:193:32: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
lf->bufSize = lf->bytesInBuf = strlen(s);
˜ ^˜˜˜˜˜˜˜˜
ucsc/linefile.c:278:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
lf->buf = needMoreMem(lf->buf, lf->bytesInBuf, newSize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/linefile.c:278:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
lf->buf = needMoreMem(lf->buf, lf->bytesInBuf, newSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/linefile.c:341:42: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
lf->lineStart = lf->lineEnd = offset - lf->bufOffsetInFile;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/linefile.c:366:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
oneSize = read(fd, buf, size);
˜˜˜˜ ^˜˜˜
ucsc/linefile.c:366:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
oneSize = read(fd, buf, size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/linefile.c:767:60: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
dyStringAppendN(lf->rawLines,line,(end - line));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
ucsc/linefile.c:778:48: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
dyStringAppendN(lf->fullLine,line,(end - line)); // includes first line's whitespace
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
ucsc/linefile.c:780:49: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
dyStringAppendN(lf->fullLine,start,(end - start));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
ucsc/linefile.c:793:48: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
dyStringAppendN(lf->rawLines,line,(end - line));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜
ucsc/linefile.c:1122:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
for (size = 0; size < chunkSize; size += lineSize)
˜˜ ^˜˜˜˜˜˜˜
16 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c:60:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
lm->blockSize = blockSize;
˜ ^˜˜˜˜˜˜˜˜
ucsc/localmem.c:61:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
lm->allignAdd = (aliSize-1);
˜ ˜˜˜˜˜˜˜^˜
ucsc/localmem.c:63:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
newBlock(lm, blockSize);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/localmem.c:83:26: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t memLeft = mb->end - mb->free;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/localmem.c:108:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *s = lmAlloc(lm, size+1);
˜˜˜˜˜˜˜ ˜˜˜˜^˜
ucsc/localmem.c:120:39: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return lmCloneStringZ(lm, string, strlen(string));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/localmem.c:133:60: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return lmCloneStringZ(lm, startFirstWord, endFirstWord - startFirstWord);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/localmem.c:159:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
n = lmAlloc(lm, size);
˜˜˜˜˜˜˜ ^˜˜˜
ucsc/localmem.c:158:38: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int size = sizeof(*n) + strlen(name) + 1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/sqlNum.c -o ucsc/sqlNum.o
ucsc/sqlNum.c:24:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
res += c - '0';
˜˜ ˜˜^˜˜˜˜
ucsc/sqlNum.c:43:14: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
res += c - '0';
˜˜ ˜˜^˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c:56:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
return 1.001*uncompressedSize + 13;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
ucsc/zlibFace.c:78:20: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
int uncSize = count*sizeof(bits32);
˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/zlibFace.c:78:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int uncSize = count*sizeof(bits32);
^˜˜˜˜˜
ucsc/zlibFace.c:81:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
testData[i] = i;
˜ ^
ucsc/zlibFace.c:82:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compBufSize = zCompBufSize(uncSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/zlibFace.c:84:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compSize = zCompress(testData, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/zlibFace.c:84:54: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int compSize = zCompress(testData, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/zlibFace.c:86:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
zUncompress(compBuf, compSize, uncBuf, uncSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/zlibFace.c:86:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
zUncompress(compBuf, compSize, uncBuf, uncSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/zlibFace.c:87:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (memcmp(uncBuf, testData, uncSize) != 0)
˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/zlibFace.c:82:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compBufSize = zCompBufSize(uncSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/zlibFace.c:84:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int compSize = zCompress(testData, uncSize, compBuf, compBufSize);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
12 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/dystring.c -o ucsc/dystring.o
ucsc/dystring.c:18:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ds->string = needMem(initialBufSize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ucsc/dystring.c:62:52: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ds->string = needMoreMem(ds->string, ds->stringSize+1, newSize+1);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ucsc/dystring.c:62:63: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ds->string = needMoreMem(ds->string, ds->stringSize+1, newSize+1);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/dystring.c:82:43: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int oldSizeTimesOneAndAHalf = oldSize * 1.5;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜˜
ucsc/dystring.c:123:29: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
dyStringAppendN(ds, string, strlen(string));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/dystring.c:184:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int len = strlen(format) * 3;
˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/dystring.c:197:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/dystring.c:197:34: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/dystring.c:197:57: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int inLen = strlen(in), outLen = strlen(out), origLen = strlen(orig);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/dystring.c:208:27: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
dyStringAppendN(dy, s, e - s);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
ucsc/dystring.c:213:27: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
dyStringAppendN(dy, s, e - s);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/hmmstats.c -o ucsc/hmmstats.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c:74:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, buf, size);
˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/obscure.c:105:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
words = needMem(wordCount * sizeof(words[0]));
^˜˜˜˜˜˜˜˜ ˜
ucsc/obscure.c:189:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *buf = needMem(bufSize);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/obscure.c:202:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((bytesRead = read(s, buf, bufSize)) > 0)
˜˜˜˜ ^˜˜˜˜˜˜
ucsc/obscure.c:204:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (write(d, buf, bytesRead) < 0)
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/obscure.c:202:21: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
while ((bytesRead = read(s, buf, bufSize)) > 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/obscure.c:229:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *buf = needMem(bufSize);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/obscure.c:233:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
readSize = read(s, buf, bufSize);
˜˜˜˜ ^˜˜˜˜˜˜
ucsc/obscure.c:235:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWriteFd(d, buf, readSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/obscure.c:233:16: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
readSize = read(s, buf, bufSize);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/obscure.c:255:10: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
return b - a;
˜˜˜˜˜˜ ˜˜^˜˜
ucsc/obscure.c:271:10: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return b - a;
˜˜˜˜˜˜ ˜˜^˜˜
ucsc/obscure.c:394:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int newSize = strlen(in) + countChars(in, toEscape);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/obscure.c:395:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *out = needMem(newSize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/obscure.c:394:26: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int newSize = strlen(in) + countChars(in, toEscape);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/obscure.c:404:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int newSize = 2 + strlen(in) + countChars(in, quoteChar);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/obscure.c:405:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *out = needMem(newSize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/obscure.c:404:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int newSize = 2 + strlen(in) + countChars(in, quoteChar);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/obscure.c:517:23: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
el = slNameNewN(s, e - s);
˜˜˜˜˜˜˜˜˜˜ ˜˜^˜˜
ucsc/obscure.c:623:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
array = needLargeMem(count * sizeof(*array));
^˜˜˜˜ ˜
ucsc/obscure.c:726:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (memcmp(name, commaList, nameLen) == 0)
˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/obscure.c:720:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nameLen = strlen(name);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/pipeline.c -o ucsc/pipeline.o
ucsc/pipeline.c:121:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
proc->cmd = needMem((cmdLen+1)*sizeof(char*));
˜˜˜˜˜˜^˜ ˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/rangeTree.c -o ucsc/rangeTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/rbTree.c -o ucsc/rbTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c:273:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
carefulAlignMask = ˜carefulAlignAdd;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/memalloc.c:296:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
aliSize = ((size + sizeof(*cmb) + 4 + carefulAlignAdd)&carefulAlignMask);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/memalloc.c:298:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
cmb->size = size;
˜ ^˜˜˜
ucsc/memalloc.c:311:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t size = cmb->size;
˜˜˜˜ ˜˜˜˜˜^˜˜˜
ucsc/memalloc.c:356:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size = cmb->size;
˜ ˜˜˜˜˜^˜˜˜
ucsc/memalloc.c:379:8: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'long' [-Wsign-conversion]
return carefulAlloced;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/dlist.c -o ucsc/dlist.o
ucsc/dlist.c:228:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
struct dlSorter *sorter = needLargeMem(len * sizeof(sorter[0])), *s;
^˜˜ ˜
ucsc/dlist.c:238:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(sorter, len, sizeof(sorter[0]), dlNodeCmp);
˜˜˜˜˜ ^˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c:131:17: warning: implicit conversion changes signedness: 'ssize_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
bits64 rd = read(sd, buf, chunkSize);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:132:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (rd < 0)
˜˜ ^ ˜
ucsc/udc.c:173:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
url, offset, (offset + size - 1));
˜ ^˜˜˜
ucsc/udc.c:232:10: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, offset, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜
ucsc/udc.c:233:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int sizeRead = fread(buffer, 1, size, f);
˜˜˜˜˜ ^˜˜˜
ucsc/udc.c:233:16: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int sizeRead = fread(buffer, 1, size, f);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:253:30: warning: implicit conversion changes signedness: '__darwin_time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
retInfo->updateTime = status.st_mtime;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
/usr/include/sys/stat.h:275:31: note: expanded from macro 'st_mtime'
#define st_mtime st_mtimespec.tv_sec
^
ucsc/udc.c:254:24: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
retInfo->size = status.st_size;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:289:10: warning: implicit conversion changes signedness: 'unsigned long long' to 'long' [-Wsign-conversion]
fseek(f, offset, SEEK_SET);
˜˜˜˜˜ ^˜˜˜˜˜
ucsc/udc.c:299:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int oneReadSize = fread(pt, 1, readChunk, f);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/udc.c:299:23: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int oneReadSize = fread(pt, 1, readChunk, f);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:324:30: warning: implicit conversion changes signedness: '__darwin_time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
retInfo->updateTime = status.st_mtime;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
/usr/include/sys/stat.h:275:31: note: expanded from macro 'st_mtime'
#define st_mtime st_mtimespec.tv_sec
^
ucsc/udc.c:325:24: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
retInfo->size = status.st_size;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:349:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((remaining > 0) && ((rd = read(sd, buf, remaining)) > 0))
˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/udc.c:360:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
ci->offset += total;
˜˜ ^˜˜˜˜
ucsc/udc.c:349:34: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
while ((remaining > 0) && ((rd = read(sd, buf, remaining)) > 0))
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:377:21: warning: implicit conversion changes signedness: 'long long' to 'unsigned long long' [-Wsign-conversion]
retInfo->size = netUrlSizeByRangeResponse(url);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:378:23: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (retInfo->size < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/udc.c:386:21: warning: implicit conversion changes signedness: 'long long' to 'unsigned long long' [-Wsign-conversion]
retInfo->size = atoll(sizeString);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:416:23: warning: implicit conversion changes signedness: 'time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
retInfo->updateTime = t;
˜ ^
ucsc/udc.c:446:17: warning: implicit conversion changes signedness: 'long long' to 'unsigned long long' [-Wsign-conversion]
retInfo->size = size;
˜ ^˜˜˜
ucsc/udc.c:447:23: warning: implicit conversion changes signedness: 'time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
retInfo->updateTime = t;
˜ ^
ucsc/udc.c:462:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *path = needMem(dirLen + nameLen + 2);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/udc.c:460:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int dirLen = strlen(file->cacheDir);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:461:15: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nameLen = strlen(fileName);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:478:49: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int blockCount = (remoteSize + udcBlockSize - 1)/udcBlockSize;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:556:28: warning: implicit conversion changes signedness: '__darwin_time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
bits->localUpdate = status.st_mtime;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
/usr/include/sys/stat.h:275:31: note: expanded from macro 'st_mtime'
#define st_mtime st_mtimespec.tv_sec
^
ucsc/udc.c:557:28: warning: implicit conversion changes signedness: '__darwin_time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
bits->localAccess = status.st_atime;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
/usr/include/sys/stat.h:274:31: note: expanded from macro 'st_atime'
#define st_atime st_atimespec.tv_sec
^
ucsc/udc.c:635:27: warning: implicit conversion changes signedness: 'unsigned long long' to 'time_t' (aka 'long') [-Wsign-conversion]
file->updateTime = bits->remoteUpdate;
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:657:45: warning: implicit conversion changes signedness: 'time_t' (aka 'long') to 'unsigned long long' [-Wsign-conversion]
udcNewCreateBitmapAndSparse(file, file->updateTime, file->size, version);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/udc.c:675:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
file->endData = initialCachedBlocks * udcBlockSize;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:671:51: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int endBlock = (file->size + udcBlockSize - 1)/udcBlockSize;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:709:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *output = needMem(size+1);
˜˜˜˜˜˜˜ ˜˜˜˜^˜
ucsc/udc.c:749:55: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
safencpy(auth, sizeof(auth), afterProtocol, userPwd+1-afterProtocol);
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:738:22: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
int colonPos = colon - url;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜
ucsc/udc.c:780:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
file->cacheDir = needMem(len);
˜˜˜˜˜˜˜ ^˜˜
ucsc/udc.c:779:79: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int len = strlen(cacheDir) + 1 + strlen(protocol) + 1 + strlen(afterProtocol) + 1;
˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/udc.c:796:17: warning: implicit conversion changes signedness: 'unsigned long long' to 'long long' [-Wsign-conversion]
ret = bits->fileSize;
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜
ucsc/udc.c:798:19: warning: implicit conversion changes signedness: 'unsigned long long' to 'time_t' (aka 'long') [-Wsign-conversion]
*retTime = bits->remoteUpdate;
˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:863:41: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
file->endData = file->size = status.st_size;
˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:870:26: warning: implicit conversion changes signedness: 'unsigned long long' to 'time_t' (aka 'long') [-Wsign-conversion]
file->updateTime = info.updateTime;
˜ ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/udc.c:984:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
offset = strlen(cacheDir);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1000:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
safef(buf, size, "%s://%s", protocol, afterProtocol);
˜˜˜˜˜ ^˜˜˜
ucsc/udc.c:1026:21: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
unsigned long now = clock1(), oldestTime = now;
˜˜˜ ^˜˜˜˜˜˜˜
ucsc/udc.c:1036:23: warning: operand of ? changes signedness: 'time_t' (aka 'long') to 'unsigned long' [-Wsign-conversion]
oldestTime = min(fileModTime(sl->name), oldestTime);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:1154:33: note: expanded from macro 'min'
#define min(a,b) ( (a) < (b) ? (a) : (b) )
^
ucsc/udc.c:1051:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Bits *bits = needLargeMem(byteSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/udc.c:1053:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustReadFd(fd, bits, byteSize);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/udc.c:1098:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 startPos = (bits64)startBlock * blockSize;
˜ ^˜˜˜˜˜˜˜˜
ucsc/udc.c:1099:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 endPos = startPos + (bits64)blockCount * blockSize;
˜ ^˜˜˜˜˜˜˜˜
ucsc/udc.c:1111:31: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
mustLseek(file->fdSparse, startPos, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/udc.c:1107:65: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int actualSize = file->prot->fetchData(file->url, startPos, readSize, buf, &(file->connInfo));
˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/udc.c:1145:80: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
fetchMissingBlocks(file, bits, nextClearBit + partOffset, clearSize, bits->blockSize);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
ucsc/udc.c:1161:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWriteFd(bits->fd, b, byteSize);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
ucsc/udc.c:1165:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*retFetchedStart = startBlock * bits->blockSize;
^˜˜˜˜˜˜˜˜˜ ˜
ucsc/udc.c:1166:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*retFetchedEnd = endBlock * bits->blockSize;
^˜˜˜˜˜˜˜ ˜
ucsc/udc.c:1124:24: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int startBlock = start / bits->blockSize;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1125:44: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int endBlock = (end + bits->blockSize - 1) / bits->blockSize;
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1207:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 s,e, endPos=offset+size;
˜^˜˜˜
ucsc/udc.c:1241:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
bits64 end = start + size;
˜ ^˜˜˜
ucsc/udc.c:1262:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
int sizeInBuf = endInBuf - start;
^˜˜˜˜˜˜˜ ˜
ucsc/udc.c:1268:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
file->offset += sizeInBuf;
˜˜ ^˜˜˜˜˜˜˜˜
ucsc/udc.c:1273:28: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
mustLseek(file->fdSparse, start, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/udc.c:1284:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
end = start + size;
˜ ^˜˜˜
ucsc/udc.c:1309:28: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
mustLseek(file->fdSparse, start, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/udc.c:1314:55: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustReadFd(file->fdSparse, file->sparseReadAheadBuf, size);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/udc.c:1320:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustReadFd(file->fdSparse, cbuf, size);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/udc.c:1321:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
file->offset += size;
˜˜ ^˜˜˜
ucsc/udc.c:1244:12: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
size = end - start;
˜ ˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:1261:25: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int endInBuf = min(raEnd, end);
˜˜˜˜˜˜˜˜ ^˜˜˜˜
ucsc/common.h:1154:33: note: expanded from macro 'min'
#define min(a,b) ( (a) < (b) ? (a) : (b) )
^
ucsc/udc.c:1261:32: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int endInBuf = min(raEnd, end);
˜˜˜˜˜˜˜˜ ^˜˜
ucsc/common.h:1154:39: note: expanded from macro 'min'
#define min(a,b) ( (a) < (b) ? (a) : (b) )
^
ucsc/udc.c:1262:31: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int sizeInBuf = endInBuf - start;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:1288:17: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
size = end - start;
˜ ˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:1316:13: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
size = end - start;
˜ ˜˜˜˜^˜˜˜˜˜˜
ucsc/udc.c:1408:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *newBuf = needLargeMem(newBufSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1414:14: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
char c = udcGetChar(file);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1438:24: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
udcMustRead(file, buf, size);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
ucsc/udc.c:1460:27: warning: implicit conversion changes signedness: 'unsigned long long' to 'off_t' (aka 'long long') [-Wsign-conversion]
mustLseek(file->fdSparse, offset, SEEK_SET);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
ucsc/udc.c:1473:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int blockSize = bits->blockSize;
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
ucsc/udc.c:1475:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
int blockCount = (bits->fileSize + blockSize - 1)/blockSize;
˜ ^˜˜˜˜˜˜˜˜
ucsc/udc.c:1475:51: warning: implicit conversion changes signedness: 'int' to 'unsigned long long' [-Wsign-conversion]
int blockCount = (bits->fileSize + blockSize - 1)/blockSize;
˜^˜˜˜˜˜˜˜˜
ucsc/udc.c:1479:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Bits *b = needLargeMem(bitmapSize);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1480:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustReadFd(bits->fd, b, bitmapSize);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1475:50: warning: implicit conversion loses integer precision: 'unsigned long long' to 'int' [-Wshorten-64-to-32]
int blockCount = (bits->fileSize + blockSize - 1)/blockSize;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/udc.c:1506:23: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
results += file->size;
˜˜ ˜˜˜˜˜˜^˜˜˜
ucsc/udc.c:1516:23: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
results += file->size;
˜˜ ˜˜˜˜˜˜^˜˜˜
ucsc/udc.c:1527:23: warning: implicit conversion changes signedness: 'off_t' (aka 'long long') to 'unsigned long long' [-Wsign-conversion]
results += file->size;
˜˜ ˜˜˜˜˜˜^˜˜˜
ucsc/udc.c:1539:39: warning: implicit conversion turns floating-point number into integer: 'double' to 'time_t' (aka 'long') [-Wconversion]
time_t maxSeconds = maxDays * 24 * 60 * 60;
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
87 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/net.c -o ucsc/net.o
ucsc/net.c:88:22: warning: implicit conversion loses integer precision: 'long' to '__darwin_suseconds_t' (aka 'int') [-Wshorten-64-to-32]
lTime.tv_usec = (long) (((msTimeout/1000)-lTime.tv_sec)*1000000);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:296:9: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return oneRead;
˜˜˜˜˜˜ ^˜˜˜˜˜˜
ucsc/net.c:299:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
totalRead += oneRead;
˜˜ ^˜˜˜˜˜˜
ucsc/net.c:294:15: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
oneRead = read(sd, buf + totalRead, size - totalRead);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:308:11: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int ret = netReadAll(sd, vBuf, size);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:343:11: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
out[i] = x;
˜ ^
ucsc/net.c:461:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
cgiDecode(parsed->user,parsed->user,strlen(parsed->user));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:462:49: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
cgiDecode(parsed->password,parsed->password,strlen(parsed->password));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:597:18: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
if ((readSize = read(sd, buf, sizeof(buf))) == 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:849:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int wt = write(params->pipefd[1], buf, rd);
˜˜˜˜˜ ^˜
ucsc/net.c:845:13: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
while((rd = read(params->sdata, buf, 32768)) > 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:848:42: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
rd = params->npu.byteRangeEnd - dataPos + 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ucsc/net.c:849:14: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
int wt = write(params->pipefd[1], buf, rd);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:1083:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWriteFd(sd, dy->string, dy->stringSize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/net.c:1221:20: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
while ((readSize = read(sd, buf, sizeof(buf))) > 0)
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:1303:10: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
nread = read(sd, &c, 1); /* one char at a time, but http headers are small */
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:2122:36: warning: implicit conversion changes signedness: 'ssize_t' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int writeCount = write(out, buf, readCount);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/net.c:1922:24: warning: implicit conversion loses integer precision: 'long long' to 'int' [-Wshorten-64-to-32]
starStep = fileSize/starMax;
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ucsc/net.c:2122:20: warning: implicit conversion loses integer precision: 'ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
int writeCount = write(out, buf, readCount);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:2264:7: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
len = length;
˜ ^˜˜˜˜˜
ucsc/net.c:2270:18: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (write(sd, s, length)<0)
˜˜˜˜˜ ^˜˜˜˜˜
ucsc/net.c:2259:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int length = strlen(s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/net.c:2289:15: warning: implicit conversion loses integer precision: 'unsigned int' to 'unsigned char' [-Wconversion]
b[0] = (length>>8);
˜ ˜˜˜˜˜˜^˜˜
ucsc/net.c:2281:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
unsigned length = strlen(s);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/net.c:2350:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (netReadAll(sd, buf, length) < 0)
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
ucsc/net.c:2350:37: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (netReadAll(sd, buf, length) < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/net.c:2340:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
sz = netReadAll(sd, &len, 1);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:2377:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s = needMem(length+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
ucsc/net.c:2379:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
if (netReadAll(sd, s, length) < 0)
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
ucsc/net.c:2379:35: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (netReadAll(sd, s, length) < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/net.c:2368:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
sz = netReadAll(sd, b, 2);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:2412:35: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (netReadAll(sd, s, length) < 0)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^ ˜
ucsc/net.c:2396:6: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
sz = netReadAll(sd, b, 4);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/net.c:2503:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWriteFd(lf->fd, dy->string, dy->stringSize);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜
34 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/bits.c -o ucsc/bits.o
ucsc/bits.c:55:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return needLargeZeroedMem(byteCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bits.c:63:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return needLargeZeroedMemResize(b, byteCount, newByteCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/bits.c:63:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
return needLargeZeroedMemResize(b, byteCount, newByteCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/bits.c:70:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
Bits* bits = needLargeZeroedMem(byteCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/twoBit.c -o ucsc/twoBit.o
ucsc/twoBit.c:72:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*starts++ = startN;
˜ ^˜˜˜˜˜
ucsc/twoBit.c:73:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*sizes++ = i - startN;
˜ ˜˜^˜˜˜˜˜˜˜
ucsc/twoBit.c:80:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*starts = startN;
˜ ^˜˜˜˜˜
ucsc/twoBit.c:81:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*sizes = i - startN;
˜ ˜˜^˜˜˜˜˜˜˜
ucsc/twoBit.c:104:18: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*starts++ = startLower;
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:105:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*sizes++ = i - startLower;
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:112:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*starts = startLower;
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:113:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
*sizes = i - startLower;
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:136:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
pt = AllocArray(twoBit->data, ubyteSize);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/twoBit.c:138:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
twoBit->size = seq->size;
˜ ˜˜˜˜˜^˜˜˜
ucsc/twoBit.c:154:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
twoBit->nBlockCount = countBlocksOfN(dna, seq->size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:165:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
twoBit->maskBlockCount = countBlocksOfLower(dna, seq->size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:189:2: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
+ sizeof(twoBit->reserved);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:181:8: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
return packedSize(twoBit->size)
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:181:27: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return packedSize(twoBit->size)
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜
ucsc/twoBit.c:215:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustWrite(f, twoBit->data, packedSize(twoBit->size));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:215:47: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
mustWrite(f, twoBit->data, packedSize(twoBit->size));
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜
ucsc/twoBit.c:224:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
bits32 seqCount = slCount(twoBitList);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:245:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
offset += nameLen + 1 + sizeof(bits32);
˜˜˜˜˜˜˜˜^˜˜ ˜
ucsc/twoBit.c:254:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
offset += size;
˜˜ ^˜˜˜
ucsc/twoBit.c:242:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nameLen = strlen(twoBit->name);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:361:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
posVal = pos[startIx];
˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:368:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
posVal = pos[midIx];
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:382:38: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
if (!bptFileFind(tbf->bpt, name, strlen(name), &offset, sizeof(offset)))
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:456:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
packByteCount = packedSize(twoBit->size);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:456:36: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
packByteCount = packedSize(twoBit->size);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜^˜˜˜
ucsc/twoBit.c:538:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
fragEnd = seqSize;
˜ ^˜˜˜˜˜˜
ucsc/twoBit.c:565:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dna = seq->dna = needLargeMem(outSize+1);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/twoBit.c:573:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
packed = packedAlloc = needLargeMem(packByteCount);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:575:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mustRead(f, packed, packByteCount);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:638:42: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int startIx = findGreatestLowerBound(nBlockCount, nStarts, fragStart);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:641:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int s = nStarts[i];
˜ ^˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:642:12: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int e = s + nSizes[i];
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:642:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int e = s + nSizes[i];
^ ˜
ucsc/twoBit.c:659:39: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int startIx = findGreatestLowerBound(maskBlockCount, maskStarts,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:663:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int s = maskStarts[i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:664:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int e = s + maskSizes[i];
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:664:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int e = s + maskSizes[i];
^ ˜
ucsc/twoBit.c:681:20: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
*retFullSize = seqSize;
˜ ^˜˜˜˜˜˜
ucsc/twoBit.c:706:8: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return readBits32(tbf->f, tbf->isSwapped);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:741:54: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
tbss->start, tbss->end));
˜˜˜˜˜˜^˜˜˜˜
ucsc/twoBit.c:741:67: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
tbss->start, tbss->end));
˜˜˜˜˜˜^˜˜
ucsc/twoBit.c:825:5: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
n = strtol(s, &e, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:833:5: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
n = strtol(s, &e, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:874:14: warning: implicit conversion loses integer precision: 'long' to 'unsigned int' [-Wshorten-64-to-32]
seq->start = strtol(s, &e, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:881:16: warning: implicit conversion loses integer precision: 'long' to 'unsigned int' [-Wshorten-64-to-32]
seq->end = strtol(s, &e, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:946:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(seqSpecs, numSeqs);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/twoBit.c:1003:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
nBlockCount = readBits32(tbf->f, tbf->isSwapped);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:1010:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(nStarts, nBlockCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/twoBit.c:1011:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(nSizes, nBlockCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/twoBit.c:1012:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mustRead(tbf->f, nStarts, sizeof(nStarts[0]) * nBlockCount);
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:1013:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mustRead(tbf->f, nSizes, sizeof(nSizes[0]) * nBlockCount);
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:1041:8: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
size = readBits32(tbf->f, tbf->isSwapped);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:1044:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
nBlockCount = readBits32(tbf->f, tbf->isSwapped);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:1052:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(nStarts, nBlockCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/twoBit.c:1053:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
AllocArray(nSizes, nBlockCount);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:240:70: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = needLargeZeroedMem(sizeof(*pt) * (size)))
^
ucsc/twoBit.c:1054:52: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mustRead(tbf->f, nStarts, sizeof(nStarts[0]) * nBlockCount);
˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/twoBit.c:1055:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mustRead(tbf->f, nSizes, sizeof(nSizes[0]) * nBlockCount);
˜ ^˜˜˜˜˜˜˜˜˜˜
58 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
ucsc/_cheapcgi.c:24:20: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
*out++ = code;
˜ ^˜˜˜
ucsc/_cheapcgi.c:53:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
outString = needMem(outSize+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/_cheapcgi.c:66:30: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
unsigned char uc = c;
˜˜ ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/internet.c -o ucsc/internet.o
ucsc/internet.c:131:15: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
quad[i] = atoi(s);
˜ ^˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/https.c -o ucsc/https.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/base64.c -o ucsc/base64.o
ucsc/base64.c:16:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *result = (char *)needMem(4*words+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/base64.c:14:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int words = (inplen+2)/3;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
ucsc/base64.c:92:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
char *result = (char *)needMem(3*words+1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ucsc/base64.c:120:28: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
result[j++]=word >> 16 & 0xFF;
˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ucsc/base64.c:121:27: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
result[j++]=word >> 8 & 0xFF;
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
ucsc/base64.c:122:22: warning: implicit conversion changes signedness: 'int' to 'char' [-Wsign-conversion]
result[j++]=word & 0xFF;
˜˜˜˜˜˜^˜˜˜˜˜
ucsc/base64.c:91:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int words = (inplen+3)/4;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/verbose.c -o ucsc/verbose.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/os.c -o ucsc/os.o
In file included from ucsc/os.c:6:
ucsc/osunix.c:183:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int dirNameSize = strlen(dir);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ucsc/osunix.c:306:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
subChar(host, '-', '_');
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:844:50: note: expanded from macro 'subChar'
#define subChar(s,old,new) (void)memSwapChar((s),strlen(s),(old),(new))
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
In file included from ucsc/os.c:6:
ucsc/osunix.c:307:1: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
subChar(host, ':', '_');
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/common.h:844:50: note: expanded from macro 'subChar'
#define subChar(s,old,new) (void)memSwapChar((s),strlen(s),(old),(new))
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
In file included from ucsc/os.c:6:
ucsc/osunix.c:383:12: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(path);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
ucsc/osunix.c:417:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
newLen = strlen(newPath);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/osunix.c:419:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int remainingLen = strlen(s);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
ucsc/osunix.c:427:30: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int lastPos = strlen(newPath)-1;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ucsc/osunix.c:501:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
attr.c_lflag &= ˜ICANON;
˜˜ ^˜˜˜˜˜˜
ucsc/osunix.c:502:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
attr.c_lflag &= ˜ECHO;
˜˜ ^˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/wildcmp.c -o ucsc/wildcmp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -g -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ucsc/_portimpl.c -o ucsc/_portimpl.o
ucsc/_portimpl.c:19:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(pathName);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ucsc/_portimpl.c:51:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
struct fileInfo *fi = needMem(sizeof(*fi) + len);
˜ ^˜˜
ucsc/_portimpl.c:50:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen(name);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
3 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 rtracklayer.so IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)
>>>>>>>
>>>>>>> FIXING LINKS FOR rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.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" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.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" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"