IRanges 1.12.5
Bioconductor Package Maintainer
| Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/IRanges | | Last Changed Rev: 61199 / Revision: 61898 | | Last Changed Date: 2011-12-08 06:21:32 -0800 (Thu, 08 Dec 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | [ OK ] |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* installing *source* package 'IRanges' ...
** libs
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c AEbufs.c -o AEbufs.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c CompressedList_class.c -o CompressedList_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DataFrame_class.c -o DataFrame_class.o
DataFrame_class.c: In function 'set_DataFrame_rownames':
DataFrame_class.c:11:1: warning: no return statement in function returning non-void
DataFrame_class.c: In function 'set_DataFrame_nrows':
DataFrame_class.c:16:1: warning: no return statement in function returning non-void
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Grouping_class.c -o Grouping_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_class.c -o IRanges_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_utils.c -o IRanges_utils.o
IRanges_utils.c: In function '_reduce_ranges':
IRanges_utils.c:77:6: warning: 'append_or_drop' may be used uninitialized in this function
IRanges_utils.c:77:22: warning: 'max_end' may be used uninitialized in this function
IRanges_utils.c:77:31: warning: 'gapwidth' may be used uninitialized in this function
IRanges_utils.c:77:41: warning: 'delta' may be used uninitialized in this function
IRanges_utils.c: In function 'IRanges_reduce':
IRanges_utils.c:137:41: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IntervalTree.c -o IntervalTree.o
IntervalTree.c: In function '_IntegerIntervalTree_overlap':
IntervalTree.c:125:8: warning: 'result_inds' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RangedData_class.c -o RangedData_class.o
RangedData_class.c: In function 'set_RangedData_ranges':
RangedData_class.c:12:1: warning: no return statement in function returning non-void
RangedData_class.c: In function 'set_RangedData_values':
RangedData_class.c:17:1: warning: no return statement in function returning non-void
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c RleViews_utils.c -o RleViews_utils.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rle_class.c -o Rle_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rle_utils.c -o Rle_utils.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SEXP_utils.c -o SEXP_utils.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SharedDouble_utils.c -o SharedDouble_utils.o
SharedDouble_utils.c: In function 'SharedDouble_new':
SharedDouble_utils.c:24:7: warning: 'tag' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SharedInteger_utils.c -o SharedInteger_utils.o
SharedInteger_utils.c: In function 'SharedInteger_new':
SharedInteger_utils.c:24:7: warning: 'tag' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SharedRaw_utils.c -o SharedRaw_utils.o
SharedRaw_utils.c: In function 'SharedRaw_new':
SharedRaw_utils.c:24:7: warning: 'tag' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SharedVector_class.c -o SharedVector_class.o
SharedVector_class.c: In function 'SharedVector_address0':
SharedVector_class.c:185:8: warning: 'address0' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SimpleList_class.c -o SimpleList_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Vector_class.c -o Vector_class.o
Vector_class.c: In function 'vector_seqselect':
Vector_class.c:95:4: warning: implicit declaration of function 'UNIMPLEMENTED_TYPE'
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XDoubleViews_utils.c -o XDoubleViews_utils.o
XDoubleViews_utils.c: In function 'get_cachedDoubleSeq_which_min':
XDoubleViews_utils.c:185:9: warning: 'cur_min' may be used uninitialized in this function
XDoubleViews_utils.c: In function 'get_cachedDoubleSeq_which_max':
XDoubleViews_utils.c:212:9: warning: 'cur_max' may be used uninitialized in this function
XDoubleViews_utils.c: In function 'XDoubleViews_summary1':
XDoubleViews_utils.c:243:11: warning: 'fun' may be used uninitialized in this function
XDoubleViews_utils.c: In function 'XDoubleViews_summary2':
XDoubleViews_utils.c:284:8: warning: 'fun' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
XIntegerViews_utils.c: In function 'get_cachedIntSeq_which_min':
XIntegerViews_utils.c:160:12: warning: 'cur_min' may be used uninitialized in this function
XIntegerViews_utils.c: In function 'get_cachedIntSeq_which_max':
XIntegerViews_utils.c:183:12: warning: 'cur_max' may be used uninitialized in this function
XIntegerViews_utils.c: In function 'XIntegerViews_summary1':
XIntegerViews_utils.c:214:8: warning: 'fun' may be used uninitialized in this function
XIntegerViews_utils.c: In function 'XIntegerViews_summary2':
XIntegerViews_utils.c:254:8: warning: 'fun' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function 'alloc_XVectorList':
XVectorList_class.c:340:40: warning: 'ans' may be used uninitialized in this function
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:426:6: warning: 'lkup_length' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_class.c -o XVector_class.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c anyMissing.c -o anyMissing.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/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
common.c:1605:5: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
common.c:1605:5: warning: too many arguments for format
common.c: In function 'mustRead':
common.c:1614:5: warning: unknown conversion type character 'l' in format
common.c:1614:5: warning: format '%s' expects type 'char *', but argument 2 has type 'long long int'
common.c:1614:5: warning: too many arguments for format
common.c: In function 'safecpy':
common.c:2007:5: warning: unknown conversion type character 'l' in format
common.c:2007:5: warning: unknown conversion type character 'l' in format
common.c:2007:5: warning: too many arguments for format
common.c: In function 'safencpy':
common.c:2016:5: warning: unknown conversion type character 'l' in format
common.c:2016:5: warning: unknown conversion type character 'l' in format
common.c:2016:5: warning: too many arguments for format
common.c: In function 'safecat':
common.c:2030:5: warning: unknown conversion type character 'l' in format
common.c:2030:5: warning: unknown conversion type character 'l' in format
common.c:2030:5: warning: too many arguments for format
common.c: In function 'safencat':
common.c:2039:5: warning: unknown conversion type character 'l' in format
common.c:2039:5: warning: unknown conversion type character 'l' in format
common.c:2039:5: warning: too many arguments for format
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c compact_bitvector.c -o compact_bitvector.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c coverage.c -o coverage.o
coverage.c: In function 'IRanges_coverage':
coverage.c:34:7: warning: 'values_buf' may be used uninitialized in this function
coverage.c:34:20: warning: 'lengths_buf' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dlist.c -o dlist.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c errabort.c -o errabort.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c int_utils.c -o int_utils.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/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
localmem.c:39:5: warning: too many arguments for format
gcc -I"E:/biocbld/bbs-2.9-bioc/R/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
memalloc.c:91:10: warning: unknown conversion type character 'l' in format
memalloc.c:91:10: warning: too many arguments for format
memalloc.c:94:14: warning: unknown conversion type character 'l' in format
memalloc.c:94:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
memalloc.c:94:14: warning: too many arguments for format
memalloc.c: In function 'needLargeMemResize':
memalloc.c:114:10: warning: unknown conversion type character 'l' in format
memalloc.c:114:10: warning: unknown conversion type character 'l' in format
memalloc.c:114:10: warning: too many arguments for format
memalloc.c:117:14: warning: unknown conversion type character 'l' in format
memalloc.c:117:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
memalloc.c:117:14: warning: too many arguments for format
memalloc.c: In function 'needHugeMem':
memalloc.c:139:14: warning: unknown conversion type character 'l' in format
memalloc.c:139:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
memalloc.c:139:14: warning: too many arguments for format
memalloc.c: In function 'needHugeMemResize':
memalloc.c:161:2: warning: unknown conversion type character 'l' in format
memalloc.c:161:2: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
memalloc.c:161:2: warning: too many arguments for format
memalloc.c: In function 'needMem':
memalloc.c:187:10: warning: unknown conversion type character 'l' in format
memalloc.c:187:10: warning: unknown conversion type character 'l' in format
memalloc.c:187:10: warning: too many arguments for format
memalloc.c:190:14: warning: unknown conversion type character 'l' in format
memalloc.c:190:14: warning: format '%d' expects type 'int', but argument 2 has type 'long long unsigned int'
memalloc.c:190:14: warning: too many arguments for format
memalloc.c: In function 'carefulAlloc':
memalloc.c:289:10: warning: unused variable 'allocRequest'
memalloc.c:288:10: warning: unused variable 'maxAlloc'
memalloc.c: In function 'carefulFree':
memalloc.c:318:14: warning: unknown conversion type character 'l' in format
memalloc.c:318:14: warning: too many arguments for format
memalloc.c:322:14: warning: unknown conversion type character 'l' in format
memalloc.c:322:14: warning: too many arguments for format
memalloc.c: In function 'carefulCheckHeap':
memalloc.c:360:18: warning: unknown conversion type character 'l' in format
memalloc.c:360:18: warning: too many arguments for format
memalloc.c:364:18: warning: unknown conversion type character 'l' in format
memalloc.c:364:18: warning: too many arguments for format
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c rbTree.c -o rbTree.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sort_utils.c -o sort_utils.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c str_utils.c -o str_utils.o
gcc -I"E:/biocbld/bbs-2.9-bioc/R/include" -O3 -Wall -std=gnu99 -mtune=core2 -c vector_copy.c -o vector_copy.o
gcc -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 IRanges_class.o IRanges_constructor.o IRanges_utils.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage.o dlist.o errabort.o int_utils.o localmem.o memalloc.o rbTree.o sort_utils.o str_utils.o vector_copy.o -LE:/biocbld/bbs-2.9-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'NROW' from package 'base' in package 'IRanges'
Creating a generic function for 'nlevels' from package 'base' 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 'head' from package 'utils' in package 'IRanges'
Creating a generic function for 'tail' from package 'utils' in package 'IRanges'
Creating a generic function for 'rev' from package 'base' in package 'IRanges'
Creating a new generic function for 'rep.int' in package 'IRanges'
Creating a generic function for 'subset' from package 'base' in package 'IRanges'
Creating a generic function for 'unique' from package 'base' in package 'IRanges'
Creating a generic function for 'as.data.frame' from package 'base' in package 'IRanges'
Creating a generic function for 'append' from package 'base' in package 'IRanges'
Creating a generic function for 'tapply' from package 'base' in package 'IRanges'
Creating a generic function for 'aggregate' from package 'stats' in package 'IRanges'
Creating a generic function for 'lapply' from package 'base' in package 'IRanges'
Creating a generic function for 'sapply' from package 'base' in package 'IRanges'
Creating a new generic function for 'mapply' 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 'relist' from package 'utils' in package 'IRanges'
Creating a generic function for 'Reduce' from package 'base' in package 'IRanges'
Creating a generic function for 'Filter' from package 'base' in package 'IRanges'
Creating a generic function for 'Find' from package 'base' in package 'IRanges'
Creating a new generic function for 'Map' in package 'IRanges'
Creating a generic function for 'Position' from package 'base' in package 'IRanges'
Creating a new generic function for 'eval' in package 'IRanges'
Creating a generic function for 'with' 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 'update' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.matrix' from package 'base' in package 'IRanges'
Creating a generic function for 'unlist' from package 'base' in package 'IRanges'
Creating a generic function for 'duplicated' from package 'base' in package 'IRanges'
Creating a new generic function for 'order' in package 'IRanges'
Creating a generic function for 'sort' from package 'base' in package 'IRanges'
Creating a generic function for 'rank' from package 'base' in package 'IRanges'
Creating a generic function for '%in%' from package 'base' in package 'IRanges'
Creating a new generic function for 'union' in package 'IRanges'
Creating a new generic function for 'intersect' in package 'IRanges'
Creating a new generic function for 'setdiff' in package 'IRanges'
Creating a generic function for 'NCOL' 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 new generic function for 'cbind' in package 'IRanges'
Creating a new generic function for 'rbind' in package 'IRanges'
Creating a generic function for 'xtabs' from package 'stats' 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.vector' from package 'base' in package 'IRanges'
Creating a generic function for 'as.factor' from package 'base' in package 'IRanges'
Creating a generic function for 'is.unsorted' from package 'base' in package 'IRanges'
Creating a generic function for 'split' from package 'base' in package 'IRanges'
Creating a generic function for 'summary' from package 'base' in package 'IRanges'
Creating a new generic function for 'table' 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 new generic function for 'pmax' in package 'IRanges'
Creating a new generic function for 'pmin' in package 'IRanges'
Creating a new generic function for 'pmax.int' in package 'IRanges'
Creating a new generic function for 'pmin.int' 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 'quantile' 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 new generic function for 'paste' in package 'IRanges'
Creating a generic function for 'levels' from package 'base' in package 'IRanges'
Creating a generic function for 'nrow' from package 'base' in package 'IRanges'
Creating a generic function for 'ncol' from package 'base' 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 'rownames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'colnames<-' from package 'base' in package 'IRanges'
Creating a generic function for 'merge' from package 'base' in package 'IRanges'
Creating a generic function for 'within' 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'
Creating a generic function for 'toString' from package 'base' in package 'IRanges'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'IRangesOverview.Rnw'
'RleTricks.Rnw'
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_1.12.5.zip
* DONE (IRanges)