Package: IRanges

Version: 1.10.6

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch IRanges_1.10.6.tar.gz

StartedAt: 2011-10-20 15:34:10 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:37:14 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 184.0 seconds

RetCode: 0

Status:  OK

CheckDir: IRanges.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/IRanges.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.10.6'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'IRanges' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: BSgenome.Celegans.UCSC.ce2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'IRanges_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'IRanges' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c AEbufs.c -o AEbufs.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c CompressedList_class.c -o CompressedList_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GappedRanges_class.c -o GappedRanges_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c Grouping_class.c -o Grouping_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c IRanges_class.c -o IRanges_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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:138:41: warning: 'ans_inframe_start' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c RleViews_utils.c -o RleViews_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c Rle_class.c -o Rle_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c Rle_utils.c -o Rle_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c SEXP_utils.c -o SEXP_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c SharedVector_class.c -o SharedVector_class.o
SharedVector_class.c: In function 'SharedVector_address0':
SharedVector_class.c:174:8: warning: 'address0' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c SimpleList_class.c -o SimpleList_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c XDoubleViews_class.c -o XDoubleViews_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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:423:6: warning: 'lkup_length' may be used uninitialized in this function
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c XVector_class.c -o XVector_class.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c anyMissing.c -o anyMissing.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c compact_bitvector.c -o compact_bitvector.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c dlist.c -o dlist.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c errabort.c -o errabort.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c int_utils.c -o int_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c rbTree.c -o rbTree.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c sort_utils.c -o sort_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c str_utils.c -o str_utils.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -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_class.o XIntegerViews_class.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˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/IRanges.Rcheck/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a new generic function for "NROW" in "IRanges"
Creating a new generic function for "nlevels" in "IRanges"
Creating a new generic function for "window" in "IRanges"
Creating a new generic function for "window<-" in "IRanges"
Creating a new generic function for "head" in "IRanges"
Creating a new generic function for "tail" in "IRanges"
Creating a new generic function for "rev" in "IRanges"
Creating a generic for 'rep.int' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Formal arguments differ: (x, ...), (x, times))
Creating a new generic function for "subset" in "IRanges"
Creating a new generic function for "append" in "IRanges"
Creating a new generic function for "tapply" in "IRanges"
Creating a new generic function for "aggregate" in "IRanges"
Creating a new generic function for "lapply" in "IRanges"
Creating a new generic function for "sapply" in "IRanges"
Creating a generic for 'mapply' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (FUN, MoreArgs, SIMPLIFY, USE.NAMES))
Creating a new generic function for "as.list" in "IRanges"
Creating a new generic function for "stack" in "IRanges"
Creating a new generic function for "relist" in "IRanges"
Creating a new generic function for "Reduce" in "IRanges"
Creating a new generic function for "Filter" in "IRanges"
Creating a new generic function for "Find" in "IRanges"
Creating a generic for 'Map' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (f))
Creating a new generic function for "Position" in "IRanges"
Creating a generic for 'eval' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Classes: "nonstandardGenericFunction", "standardGeneric")
Creating a new generic function for "with" in "IRanges"
Creating a new generic function for "start" in "IRanges"
Creating a new generic function for "end" in "IRanges"
Creating a new generic function for "update" in "IRanges"
Creating a new generic function for "as.matrix" in "IRanges"
Creating a new generic function for "as.data.frame" in "IRanges"
Creating a new generic function for "unlist" in "IRanges"
Creating a new generic function for "duplicated" in "IRanges"
Creating a new generic function for "unique" in "IRanges"
Creating a generic for 'order' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (na.last, decreasing))
Creating a new generic function for "sort" in "IRanges"
Creating a new generic function for "rank" in "IRanges"
Creating a new generic function for "%in%" in "IRanges"
Creating a generic for 'union' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Formal arguments differ: (x, y, ...), (x, y))
Creating a generic for 'intersect' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Formal arguments differ: (x, y, ...), (x, y))
Creating a generic for 'setdiff' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Formal arguments differ: (x, y, ...), (x, y))
Creating a new generic function for "NCOL" in "IRanges"
Creating a new generic function for "na.omit" in "IRanges"
Creating a new generic function for "na.exclude" in "IRanges"
Creating a new generic function for "complete.cases" in "IRanges"
Creating a generic for 'cbind' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (deparse.level))
Creating a generic for 'rbind' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (deparse.level))
Creating a new generic function for "xtabs" in "IRanges"
Creating a new generic function for "as.vector" in "IRanges"
Creating a new generic function for "as.factor" in "IRanges"
Creating a new generic function for "is.unsorted" in "IRanges"
Creating a new generic function for "split" in "IRanges"
Creating a new generic function for "summary" in "IRanges"
Creating a generic for 'table' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Formal arguments differ: (...), (..., exclude, useNA, dnn, deparse.level))
Creating a new generic function for "which" in "IRanges"
Creating a new generic function for "ifelse" in "IRanges"
Creating a new generic function for "diff" in "IRanges"
Creating a generic for 'pmax' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (na.rm))
Creating a generic for 'pmin' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (na.rm))
Creating a generic for 'pmax.int' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (na.rm))
Creating a generic for 'pmin.int' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (na.rm))
Creating a new generic function for "mean" in "IRanges"
Creating a new generic function for "var" in "IRanges"
Creating a new generic function for "cov" in "IRanges"
Creating a new generic function for "cor" in "IRanges"
Creating a new generic function for "sd" in "IRanges"
Creating a new generic function for "median" in "IRanges"
Creating a new generic function for "quantile" in "IRanges"
Creating a new generic function for "mad" in "IRanges"
Creating a new generic function for "IQR" in "IRanges"
Creating a new generic function for "smoothEnds" in "IRanges"
Creating a new generic function for "runmed" in "IRanges"
Creating a new generic function for "nchar" in "IRanges"
Creating a new generic function for "substr" in "IRanges"
Creating a new generic function for "substring" in "IRanges"
Creating a new generic function for "chartr" in "IRanges"
Creating a new generic function for "tolower" in "IRanges"
Creating a new generic function for "toupper" in "IRanges"
Creating a new generic function for "sub" in "IRanges"
Creating a new generic function for "gsub" in "IRanges"
Creating a generic for 'paste' in package 'IRanges'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (sep, collapse))
Creating a new generic function for "levels" in "IRanges"
Creating a new generic function for "which.max" in "IRanges"
Creating a new generic function for "which.min" in "IRanges"
Creating a new generic function for "nrow" in "IRanges"
Creating a new generic function for "ncol" in "IRanges"
Creating a new generic function for "rownames" in "IRanges"
Creating a new generic function for "colnames" in "IRanges"
Creating a new generic function for "rownames<-" in "IRanges"
Creating a new generic function for "colnames<-" in "IRanges"
Creating a new generic function for "merge" in "IRanges"
Creating a new generic function for "within" in "IRanges"
Creating a new generic function for "as.table" in "IRanges"
Creating a new generic function for "t" in "IRanges"
Creating a new generic function for "toString" in "IRanges"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (IRanges)

name	user	system	elapsed
AtomicList-class	0.36	0.00	0.39
DataFrame-class	0.42	0.00	0.44
DataTable-API	0	0	0
DataTable-stats	0.02	0.00	0.01
FilterRules-class	0.03	0.00	0.03
GappedRanges-class	0.17	0.00	0.21
Grouping-class	0.08	0.00	0.07
IRanges-class	1.64	0.13	1.78
IRanges-constructor	0.06	0.00	0.06
IRanges-setops	0.20	0.00	0.21
IRanges-utils	1.72	0.13	2.62
IRangesList-class	0.05	0.00	0.05
IntervalTree-class	0.16	0.00	0.16
List-class	0	0	0
MaskCollection-class	0.17	0.00	0.17
RDApplyParams-class	0.62	0.00	0.62
RangedData-class	1.42	0.00	1.42
RangedData-utils	0.08	0.00	0.08
RangedDataList-class	0.03	0.00	0.03
RangedSelection-class	0.04	0.00	0.03
Ranges-class	0.04	0.00	0.05
Ranges-comparison	0.03	0.00	0.03
Ranges-utils	0.11	0.00	0.11
RangesList-class	0.16	0.00	0.16
RangesList-utils	0.39	0.00	0.42
RangesMatching-class	0	0	0
Rle-class	0.11	0.00	0.11
RleViews-class	0.05	0.00	0.05
RleViewsList-class	0.06	0.00	0.06
SimpleList-class	0	0	0
Vector-class	0.01	0.00	0.01
Views-class	0.22	0.00	0.22
Views-utils	0.05	0.00	0.05
XIntegerViews-class	0.03	0.00	0.03
XVector-class	0.05	0.00	0.05
compact	0.50	0.01	0.64
coverage	0.08	0.00	0.08
disjoin	0.01	0.00	0.01
endoapply	0	0	0
isConstant	0.02	0.00	0.02
nearest	0.01	0.00	0.01
read.Mask	0.05	0.02	0.07
reverse	0.05	0.00	0.04
runstat	0.02	0.00	0.01
seqapply	0.06	0.00	0.07
strutils	0	0	0