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Package 236/462HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.11.1
Biocore Team c/o BioC user list
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges
Last Changed Rev: 55009 / Revision: 55359
Last Changed Date: 2011-04-20 22:58:51 -0700 (Wed, 20 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: IRanges
Version: 1.11.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IRanges_1.11.1.tar.gz
StartedAt: 2011-05-09 15:15:19 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 15:19:12 -0700 (Mon, 09 May 2011)
EllapsedTime: 232.9 seconds
RetCode: 0
Status:  OK 
CheckDir: IRanges.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘1.11.1’
* checking package name space 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 for sufficient/correct file permissions ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 sizes of PDF files under ‘inst/doc’ ... 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

IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c AEbufs.c -o AEbufs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c CompressedList_class.c -o CompressedList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c DataFrame_class.c -o DataFrame_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c GappedRanges_class.c -o GappedRanges_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Grouping_class.c -o Grouping_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c IRanges_class.c -o IRanges_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c IRanges_constructor.c -o IRanges_constructor.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c IRanges_utils.c -o IRanges_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c IntervalTree.c -o IntervalTree.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c R_init_IRanges.c -o R_init_IRanges.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c RangedData_class.c -o RangedData_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c RleViews_utils.c -o RleViews_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Rle_class.c -o Rle_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Rle_utils.c -o Rle_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SEXP_utils.c -o SEXP_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SharedDouble_utils.c -o SharedDouble_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SharedInteger_utils.c -o SharedInteger_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SharedRaw_utils.c -o SharedRaw_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SharedVector_class.c -o SharedVector_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SimpleList_class.c -o SimpleList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Vector_class.c -o Vector_class.o
Vector_class.c: In function ‘vector_seqselect’:
Vector_class.c:95: warning: implicit declaration of function ‘UNIMPLEMENTED_TYPE’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c XDoubleViews_class.c -o XDoubleViews_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c XIntegerViews_class.c -o XIntegerViews_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c XVectorList_class.c -o XVectorList_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c XVector_class.c -o XVector_class.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c anyMissing.c -o anyMissing.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c common.c -o common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c compact_bitvector.c -o compact_bitvector.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c coverage.c -o coverage.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c dlist.c -o dlist.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c errabort.c -o errabort.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c int_utils.c -o int_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c localmem.c -o localmem.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c memalloc.c -o memalloc.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c rbTree.c -o rbTree.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c sort_utils.c -o sort_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c str_utils.c -o str_utils.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c vector_copy.c -o vector_copy.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o IRanges.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-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 ...
*** tangling vignette sources ...
   ‘IRangesOverview.Rnw’ 
   ‘RleTricks.Rnw’ 
** testing if installed package can be loaded

* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.5650.0050.572
DataFrame-class0.6670.0130.694
DataTable-API0.0010.0000.001
DataTable-stats0.0220.0010.022
FilterRules-class0.1240.0010.125
GappedRanges-class0.2610.0050.266
Grouping-class0.1370.0060.142
IRanges-class2.1360.5902.792
IRanges-constructor0.0860.0050.092
IRanges-setops0.3090.0130.323
IRanges-utils2.2440.6292.940
IRangesList-class0.0710.0010.072
IntervalTree-class0.2270.0070.237
List-class0.0090.0000.010
MaskCollection-class0.2450.0030.250
RDApplyParams-class0.9510.0040.985
RangedData-class2.1320.0122.170
RangedData-utils0.1170.0010.118
RangedDataList-class0.0560.0000.057
RangedSelection-class0.0300.0010.031
Ranges-class0.0930.0040.097
Ranges-comparison0.0380.0010.039
Ranges-utils0.1750.0050.180
RangesList-class0.2410.0040.248
RangesList-utils0.6120.0070.622
RangesMatching-class0.0140.0000.015
Rle-class0.1690.0020.172
RleViews-class0.0740.0010.078
RleViewsList-class0.0940.0000.096
SimpleList-class0.0080.0000.012
Vector-class0.0090.0000.009
Views-class0.3350.0090.353
Views-utils0.0720.0020.074
XIntegerViews-class0.0500.0010.052
XVector-class0.0670.0060.072
coverage0.1100.0010.111
disjoin0.0240.0000.025
endoapply0.0140.0000.016
isConstant0.0050.0010.006
nearest0.0460.0010.047
read.Mask0.0760.0040.081
reverse0.0850.0010.087
runstat0.0520.0000.052
seqapply0.0840.0000.088
strutils0.0020.0010.003