IRanges 1.22.10
Bioconductor Package Maintainer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/IRanges | | Last Changed Rev: 92937 / Revision: 95116 | | Last Changed Date: 2014-07-28 13:34:45 -0700 (Mon, 28 Jul 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ OK ] | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/IRanges_1.22.10.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch IRanges_1.22.10.tar.gz && rm IRanges_1.22.10.tar.gz
###
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install for i386
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'IRanges' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c AEbufs.c -o AEbufs.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DataFrame_class.c -o DataFrame_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Hits_class.c -o Hits_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap_first':
IntervalTree.c:500:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap_last':
IntervalTree.c:574:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:365:3: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
IntervalTree.c: In function '_IntegerIntervalForest_overlap':
IntervalTree.c:393:17: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RangedData_class.c -o RangedData_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'compute_CHARSXP_runs':
Rle_class.c:132:31: warning: 'val0' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rle_utils.c -o Rle_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SEXP_utils.c -o SEXP_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SimpleList_class.c -o SimpleList_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Vector_class.c -o Vector_class.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
common.c: In function 'mustWrite':
common.c:1605:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1605:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1605:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'mustRead':
common.c:1614:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1614:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1614:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecpy':
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencpy':
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecat':
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencat':
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c compact_bitvector.c -o compact_bitvector.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:501:37: warning: 'x_end' may be used uninitialized in this function [-Wuninitialized]
coverage_methods.c:417:21: note: 'x_end' was declared here
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dlist.c -o dlist.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c errabort.c -o errabort.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hash_utils.c -o hash_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c int_utils.c -o int_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:166:11: warning: 'gapwidth' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c localmem.c -o localmem.o
localmem.c: In function 'newBlock':
localmem.c:39:5: warning: unknown conversion type character 'l' in format [-Wformat]
localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c memalloc.c -o memalloc.o
memalloc.c: In function 'needLargeMem':
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needLargeMemResize':
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMem':
memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMemResize':
memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needMem':
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat]
memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulAlloc':
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
memalloc.c: In function 'carefulFree':
memalloc.c:316:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:320:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:320:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulCheckHeap':
memalloc.c:358:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:362:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:362:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rbTree.c -o rbTree.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c safe_arithm.c -o safe_arithm.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sort_utils.c -o sort_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c str_utils.c -o str_utils.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ucsc_handlers.c -o ucsc_handlers.o
gcc -m32 -shared -s -static-libgcc -o IRanges.dll tmp.def AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'head' from package 'utils' in package 'IRanges'
Creating a generic function for 'tail' from package 'utils' in package 'IRanges'
Creating a generic function for 'window' from package 'stats' in package 'IRanges'
Creating a generic function for 'window<-' from package 'stats' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
Creating a generic function for 'subset' from package 'base' in package 'IRanges'
Creating a generic function for 'with' from package 'base' in package 'IRanges'
Creating a generic function for 'aggregate' from package 'stats' in package 'IRanges'
Creating a generic function for '%in%' from package 'base' in package 'IRanges'
Creating a new generic function for 'findMatches' in package 'IRanges'
Creating a generic function for 'as.list' from package 'base' in package 'IRanges'
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
Creating a generic function for 'within' from package 'base' in package 'IRanges'
Creating a generic function for 'start' from package 'stats' in package 'IRanges'
Creating a generic function for 'end' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.matrix' from package 'base' in package 'IRanges'
Creating a generic function for 'na.omit' from package 'stats' in package 'IRanges'
Creating a generic function for 'na.exclude' from package 'stats' in package 'IRanges'
Creating a generic function for 'complete.cases' from package 'stats' in package 'IRanges'
Creating a generic function for 'merge' from package 'base' in package 'IRanges'
Creating a generic function for 'by' from package 'base' in package 'IRanges'
Creating a generic function for 'mean' from package 'base' in package 'IRanges'
Creating a generic function for 'which.max' from package 'base' in package 'IRanges'
Creating a generic function for 'which.min' from package 'base' in package 'IRanges'
Creating a generic function for 'as.factor' from package 'base' in package 'IRanges'
Creating a generic function for 'which' from package 'base' in package 'IRanges'
Creating a generic function for 'ifelse' from package 'base' in package 'IRanges'
Creating a generic function for 'diff' from package 'base' in package 'IRanges'
Creating a generic function for 'var' from package 'stats' in package 'IRanges'
Creating a generic function for 'cov' from package 'stats' in package 'IRanges'
Creating a generic function for 'cor' from package 'stats' in package 'IRanges'
Creating a generic function for 'sd' from package 'stats' in package 'IRanges'
Creating a generic function for 'median' from package 'stats' in package 'IRanges'
Creating a generic function for 'mad' from package 'stats' in package 'IRanges'
Creating a generic function for 'IQR' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'nchar' from package 'base' in package 'IRanges'
Creating a generic function for 'substr' from package 'base' in package 'IRanges'
Creating a generic function for 'substring' from package 'base' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
Creating a generic function for 'levels' from package 'base' in package 'IRanges'
Creating a generic function for 'droplevels' from package 'base' in package 'IRanges'
Creating a generic function for 'split' from package 'base' in package 'IRanges'
Creating a generic function for 'unsplit' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'quantile' from package 'stats' in package 'IRanges'
Creating a generic function for 'rownames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'colnames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'as.table' from package 'base' in package 'IRanges'
Creating a generic function for 't' from package 'base' in package 'IRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'IRanges' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c AEbufs.c -o AEbufs.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DataFrame_class.c -o DataFrame_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Hits_class.c -o Hits_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap_first':
IntervalTree.c:500:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap_last':
IntervalTree.c:574:20: warning: variable 'nhits' set but not used [-Wunused-but-set-variable]
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:365:3: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
IntervalTree.c: In function '_IntegerIntervalForest_overlap':
IntervalTree.c:393:17: warning: 'result_inds' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RangedData_class.c -o RangedData_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Ranges_class.c -o Ranges_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Ranges_comparison.c -o Ranges_comparison.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'compute_CHARSXP_runs':
Rle_class.c:132:31: warning: 'val0' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Rle_utils.c -o Rle_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SEXP_utils.c -o SEXP_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SimpleList_class.c -o SimpleList_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Vector_class.c -o Vector_class.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c common.c -o common.o
common.c: In function 'mustWrite':
common.c:1605:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1605:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1605:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'mustRead':
common.c:1614:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:1614:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat]
common.c:1614:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecpy':
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2007:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencpy':
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2016:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safecat':
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2030:5: warning: too many arguments for format [-Wformat-extra-args]
common.c: In function 'safencat':
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: unknown conversion type character 'l' in format [-Wformat]
common.c:2039:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c compact_bitvector.c -o compact_bitvector.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:501:37: warning: 'x_end' may be used uninitialized in this function [-Wuninitialized]
coverage_methods.c:417:21: note: 'x_end' was declared here
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dlist.c -o dlist.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c errabort.c -o errabort.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hash_utils.c -o hash_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c int_utils.c -o int_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:177:21: warning: 'revmap_elt' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:183:35: warning: 'delta' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:166:11: warning: 'gapwidth' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:168:14: warning: 'max_end' may be used uninitialized in this function [-Wuninitialized]
inter_range_methods.c:143:6: warning: 'append_or_drop' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c localmem.c -o localmem.o
localmem.c: In function 'newBlock':
localmem.c:39:5: warning: unknown conversion type character 'l' in format [-Wformat]
localmem.c:39:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c memalloc.c -o memalloc.o
memalloc.c: In function 'needLargeMem':
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:91:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:94:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:94:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:94:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needLargeMemResize':
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:114:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:117:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:117:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:117:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMem':
memalloc.c:139:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:139:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:139:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needHugeMemResize':
memalloc.c:161:2: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:161:2: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:161:2: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'needMem':
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:187:10: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:190:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:190:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:190:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulAlloc':
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'size_t' [-Wformat]
memalloc.c:291:2: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
memalloc.c: In function 'carefulFree':
memalloc.c:316:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:316:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:320:14: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:320:14: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c: In function 'carefulCheckHeap':
memalloc.c:358:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:358:18: warning: too many arguments for format [-Wformat-extra-args]
memalloc.c:362:18: warning: unknown conversion type character 'l' in format [-Wformat]
memalloc.c:362:18: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c rbTree.c -o rbTree.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c safe_arithm.c -o safe_arithm.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sort_utils.c -o sort_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c str_utils.c -o str_utils.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ucsc_handlers.c -o ucsc_handlers.o
gcc -m64 -shared -s -static-libgcc -o IRanges.dll tmp.def AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/IRanges/libs/x64
** testing if installed package can be loaded
* DONE (IRanges)