rtracklayer 1.8.1
Michael Lawrence
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/rtracklayer | | Last Changed Rev: 48426 / Revision: 49923 | | Last Changed Date: 2010-07-26 11:43:59 -0700 (Mon, 26 Jul 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | [ OK ] | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for file 'rtracklayer/DESCRIPTION' ... OK
* preparing 'rtracklayer':
* checking DESCRIPTION meta-information ... OK
* cleaning src
rm -f IRanges_stubs.o R_init_rtracklayer.o bigWig.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.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/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o
* installing the package to re-build vignettes
* installing *source* package 'rtracklayer' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c R_init_rtracklayer.c -o R_init_rtracklayer.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c bigWig.c -o bigWig.o
bigWig.c: In function 'BWGFile_query':
bigWig.c:189: warning: 'ans_score' may be used uninitialized in this function
bigWig.c: In function 'BWGSectionList_add':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/bbiRead.c -o ucsc/bbiRead.o
ucsc/bbiRead.c: In function 'bbiSummaryArrayExtended':
ucsc/bbiRead.c:552: warning: implicit declaration of function 'bzero'
ucsc/bbiRead.c:552: warning: incompatible implicit declaration of built-in function 'bzero'
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/bbiRead.c: In function 'bbiFileOpen':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
ucsc/bbiWrite.c: In function 'bbiSummarySimpleReduce':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/bbiWrite.c: In function 'bbiChromUsageFromBedFile':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
ucsc/bwgCreate.c: In function 'bwgParseWig':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
ucsc/bwgQuery.c: In function 'bigWigIntervalQuery':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/cirTree.c -o ucsc/cirTree.o
ucsc/cirTree.c: In function 'rTreeFromChromRangeArray':
ucsc/cirTree.c:234: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:234: warning: too many arguments for format
ucsc/cirTree.c: In function 'writeTreeToOpenFile':
ucsc/cirTree.c:315: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:315: warning: too many arguments for format
ucsc/cirTree.c:330: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:330: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:330: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
ucsc/cirTree.c:330: warning: format '%s' expects type 'char *', but argument 3 has type 'long long unsigned int'
ucsc/cirTree.c:330: warning: too many arguments for format
ucsc/cirTree.c: In function 'rFindOverlappingBlocks':
ucsc/cirTree.c:497: warning: unknown conversion type character 'l' in format
ucsc/cirTree.c:497: warning: format '%u' expects type 'unsigned int', but argument 3 has type 'long long unsigned int'
ucsc/cirTree.c:497: warning: too many arguments for format
ucsc/cirTree.c: In function 'cirTreeFileBulkIndexToOpenFile':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function 'mustWrite':
ucsc/common.c:1835: warning: unknown conversion type character 'l' in format
ucsc/common.c:1835: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/common.c:1835: warning: too many arguments for format
ucsc/common.c: In function 'mustRead':
ucsc/common.c:1846: warning: unknown conversion type character 'l' in format
ucsc/common.c:1846: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/common.c:1846: warning: too many arguments for format
ucsc/common.c:1848: warning: unknown conversion type character 'l' in format
ucsc/common.c:1848: warning: too many arguments for format
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.c:2069: warning: unknown conversion type character 'l' in format
ucsc/common.c:2069: warning: unknown conversion type character 'l' in format
ucsc/common.c:2069: warning: too many arguments for format
ucsc/common.c: In function 'safecpy':
ucsc/common.c:2505: warning: unknown conversion type character 'l' in format
ucsc/common.c:2505: warning: unknown conversion type character 'l' in format
ucsc/common.c:2505: warning: too many arguments for format
ucsc/common.c: In function 'safencpy':
ucsc/common.c:2514: warning: unknown conversion type character 'l' in format
ucsc/common.c:2514: warning: unknown conversion type character 'l' in format
ucsc/common.c:2514: warning: too many arguments for format
ucsc/common.c: In function 'safecat':
ucsc/common.c:2528: warning: unknown conversion type character 'l' in format
ucsc/common.c:2528: warning: unknown conversion type character 'l' in format
ucsc/common.c:2528: warning: too many arguments for format
ucsc/common.c: In function 'safencat':
ucsc/common.c:2537: warning: unknown conversion type character 'l' in format
ucsc/common.c:2537: warning: unknown conversion type character 'l' in format
ucsc/common.c:2537: warning: too many arguments for format
ucsc/common.c: In function 'byteSwap64':
ucsc/common.c:2169: warning: array subscript is above array bounds
ucsc/common.c:2170: warning: array subscript is above array bounds
ucsc/common.c:2171: warning: array subscript is above array bounds
ucsc/common.c:2172: warning: array subscript is above array bounds
ucsc/common.c:2173: warning: array subscript is above array bounds
ucsc/common.c:2174: warning: array subscript is above array bounds
ucsc/common.c:2175: warning: array subscript is above array bounds
ucsc/common.c:2176: warning: array subscript is above array bounds
ucsc/common.c: In function 'memReadBits64':
ucsc/common.c:2169: warning: array subscript is above array bounds
ucsc/common.c:2170: warning: array subscript is above array bounds
ucsc/common.c:2171: warning: array subscript is above array bounds
ucsc/common.c:2172: warning: array subscript is above array bounds
ucsc/common.c:2173: warning: array subscript is above array bounds
ucsc/common.c:2174: warning: array subscript is above array bounds
ucsc/common.c:2175: warning: array subscript is above array bounds
ucsc/common.c:2176: warning: array subscript is above array bounds
ucsc/common.c: In function 'byteSwapDouble':
ucsc/common.c:2273: warning: array subscript is above array bounds
ucsc/common.c:2274: warning: array subscript is above array bounds
ucsc/common.c:2275: warning: array subscript is above array bounds
ucsc/common.c:2276: warning: array subscript is above array bounds
ucsc/common.c:2277: warning: array subscript is above array bounds
ucsc/common.c:2278: warning: array subscript is above array bounds
ucsc/common.c:2279: warning: array subscript is above array bounds
ucsc/common.c:2280: warning: array subscript is above array bounds
ucsc/common.c: In function 'memReadDouble':
ucsc/common.c:2273: warning: array subscript is above array bounds
ucsc/common.c:2274: warning: array subscript is above array bounds
ucsc/common.c:2275: warning: array subscript is above array bounds
ucsc/common.c:2276: warning: array subscript is above array bounds
ucsc/common.c:2277: warning: array subscript is above array bounds
ucsc/common.c:2278: warning: array subscript is above array bounds
ucsc/common.c:2279: warning: array subscript is above array bounds
ucsc/common.c:2280: warning: array subscript is above array bounds
ucsc/common.c: In function 'refListFromSlList':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
ucsc/common.c: In function 'slNameListFromStringArray':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
ucsc/common.c: In function 'slNameCloneList':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
ucsc/common.c: In function 'readDouble':
ucsc/common.c:2273: warning: array subscript is above array bounds
ucsc/common.c:2274: warning: array subscript is above array bounds
ucsc/common.c:2275: warning: array subscript is above array bounds
ucsc/common.c:2276: warning: array subscript is above array bounds
ucsc/common.c:2277: warning: array subscript is above array bounds
ucsc/common.c:2278: warning: array subscript is above array bounds
ucsc/common.c:2279: warning: array subscript is above array bounds
ucsc/common.c:2280: warning: array subscript is above array bounds
ucsc/common.c: In function 'readBits64':
ucsc/common.c:2169: warning: array subscript is above array bounds
ucsc/common.c:2170: warning: array subscript is above array bounds
ucsc/common.c:2171: warning: array subscript is above array bounds
ucsc/common.c:2172: warning: array subscript is above array bounds
ucsc/common.c:2173: warning: array subscript is above array bounds
ucsc/common.c:2174: warning: array subscript is above array bounds
ucsc/common.c:2175: warning: array subscript is above array bounds
ucsc/common.c:2176: warning: array subscript is above array bounds
ucsc/common.c: In function 'slNameListFromString':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
ucsc/common.c: In function 'slPairFromString':
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
ucsc/common.c: In function 'slNameLoadReal':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
ucsc/common.c: In function 'fileOffsetSizeMerge':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.c:294: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.c:282: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/errabort.c -o ucsc/errabort.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/hash.c -o ucsc/hash.o
ucsc/hash.c: In function 'hashElListHash':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/linefile.c -o ucsc/linefile.o
ucsc/linefile.c:34: warning: 'getDecompressor' defined but not used
ucsc/linefile.c:102: warning: 'headerBytes' defined but not used
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/localmem.c -o ucsc/localmem.o
ucsc/localmem.c: In function 'newBlock':
ucsc/localmem.c:39: warning: unknown conversion type character 'l' in format
ucsc/localmem.c:39: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/sqlNum.c -o ucsc/sqlNum.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/zlibFace.c -o ucsc/zlibFace.o
ucsc/zlibFace.c: In function 'zCompress':
ucsc/zlibFace.c:49: warning: unknown conversion type character 'l' in format
ucsc/zlibFace.c:49: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/zlibFace.c:49: warning: too many arguments for format
ucsc/zlibFace.c: In function 'zUncompress':
ucsc/zlibFace.c:70: warning: unknown conversion type character 'l' in format
ucsc/zlibFace.c:70: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
ucsc/zlibFace.c:70: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/dystring.c -o ucsc/dystring.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/hmmstats.c -o ucsc/hmmstats.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/obscure.c -o ucsc/obscure.o
ucsc/obscure.c: In function 'sprintLongWithCommas':
ucsc/obscure.c:545: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:545: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:545: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:545: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:545: warning: too many arguments for format
ucsc/obscure.c:553: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:553: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:553: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:553: warning: too many arguments for format
ucsc/obscure.c:559: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:559: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:559: warning: too many arguments for format
ucsc/obscure.c:562: warning: unknown conversion type character 'l' in format
ucsc/obscure.c:562: warning: too many arguments for format
ucsc/obscure.c: In function 'charSepToSlNames':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/obscure.c: In function 'stringToSlNames':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/obscure.c: In function 'readAllLines':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/pipeline.c -o ucsc/pipeline.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/rangeTree.c -o ucsc/rangeTree.o
ucsc/rangeTree.c: In function 'rangeListAdd':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/rbTree.c -o ucsc/rbTree.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/memalloc.c -o ucsc/memalloc.o
ucsc/memalloc.c: In function 'needLargeMem':
ucsc/memalloc.c:91: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:91: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:91: warning: too many arguments for format
ucsc/memalloc.c:94: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:94: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
ucsc/memalloc.c:94: warning: too many arguments for format
ucsc/memalloc.c: In function 'needLargeMemResize':
ucsc/memalloc.c:114: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:114: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:114: warning: too many arguments for format
ucsc/memalloc.c:117: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:117: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
ucsc/memalloc.c:117: warning: too many arguments for format
ucsc/memalloc.c: In function 'needHugeMem':
ucsc/memalloc.c:139: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:139: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
ucsc/memalloc.c:139: warning: too many arguments for format
ucsc/memalloc.c: In function 'needHugeMemResize':
ucsc/memalloc.c:161: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:161: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
ucsc/memalloc.c:161: warning: too many arguments for format
ucsc/memalloc.c: In function 'needMem':
ucsc/memalloc.c:187: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:187: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:187: warning: too many arguments for format
ucsc/memalloc.c:190: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:190: warning: format '%d' expects type 'int', but argument 2 has type 'size_t'
ucsc/memalloc.c:190: warning: too many arguments for format
ucsc/memalloc.c: In function 'carefulFree':
ucsc/memalloc.c:318: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:318: warning: too many arguments for format
ucsc/memalloc.c:322: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:322: warning: too many arguments for format
ucsc/memalloc.c: In function 'carefulCheckHeap':
ucsc/memalloc.c:360: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:360: warning: too many arguments for format
ucsc/memalloc.c:364: warning: unknown conversion type character 'l' in format
ucsc/memalloc.c:364: warning: too many arguments for format
ucsc/memalloc.c: In function 'pushMemHandler':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/memalloc.c: In function 'pushCarefulMemHandler':
ucsc/common.h:359: warning: dereferencing pointer 'n' does break strict-aliasing rules
ucsc/common.h:358: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/memalloc.c: In function 'memTrackerStart':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/dlist.c -o ucsc/dlist.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function 'udcDataViaLocal':
ucsc/udc.c:188: warning: unknown conversion type character 'l' in format
ucsc/udc.c:188: warning: format '%s' expects type 'char *', but argument 4 has type 'long long unsigned int'
ucsc/udc.c:188: warning: too many arguments for format
ucsc/udc.c:195: warning: unknown conversion type character 'l' in format
ucsc/udc.c:195: warning: too many arguments for format
ucsc/udc.c: In function 'udcDataViaSlow':
ucsc/udc.c:244: warning: unknown conversion type character 'l' in format
ucsc/udc.c:244: warning: format '%s' expects type 'char *', but argument 4 has type 'long long unsigned int'
ucsc/udc.c:244: warning: too many arguments for format
ucsc/udc.c:262: warning: unknown conversion type character 'l' in format
ucsc/udc.c:262: warning: too many arguments for format
ucsc/udc.c: In function 'udcNewCreateBitmapAndSparse':
ucsc/udc.c:439: warning: unknown conversion type character 'l' in format
ucsc/udc.c:439: warning: format '%d' expects type 'int', but argument 3 has type 'long long int'
ucsc/udc.c:439: warning: too many arguments for format
ucsc/udc.c: In function 'fetchMissingBlocks':
ucsc/udc.c:994: warning: unknown conversion type character 'l' in format
ucsc/udc.c:994: warning: format '%s' expects type 'char *', but argument 2 has type 'long long unsigned int'
ucsc/udc.c:994: warning: unknown conversion type character 'l' in format
ucsc/udc.c:994: warning: format '%d' expects type 'int', but argument 3 has type 'char *'
ucsc/udc.c:994: warning: too many arguments for format
ucsc/udc.c: In function 'udcFileCacheFiles':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/net.c -o ucsc/net.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/bits.c -o ucsc/bits.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/internet.c -o ucsc/internet.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/https.c -o ucsc/https.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/base64.c -o ucsc/base64.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/verbose.c -o ucsc/verbose.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/os.c -o ucsc/os.o
In file included from ucsc/os.c:4:
ucsc/oswin9x.c: In function 'listDirX':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/oswin9x.c:154: warning: 'currentDir' may be used uninitialized in this function
ucsc/oswin9x.c: In function 'listDir':
ucsc/common.h:360: warning: dereferencing pointer 'ppt' does break strict-aliasing rules
ucsc/common.h:357: note: initialized from here
ucsc/oswin9x.c:99: warning: 'currentDir' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/wildcmp.c -o ucsc/wildcmp.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -I"D:/biocbld/bbs-2.6-bioc/R/library/IRanges/include" -O2 -Wall -std=gnu99 -c ucsc/_portimpl.c -o ucsc/_portimpl.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o rtracklayer.dll tmp.def IRanges_stubs.o R_init_rtracklayer.o bigWig.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.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/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lRzlib -lws2_32 -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/tmpdir/Rinst202860763/rtracklayer/libs/x64
... done
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: bitops
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (rtracklayer)
* creating vignettes ... OK
* cleaning src
rm -f IRanges_stubs.o R_init_rtracklayer.o bigWig.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.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/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'rtracklayer_1.8.1.tar.gz'