Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H [I] J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.12: CHECK report for IRanges on petty

This page was generated on 2013-10-09 09:39:23 -0700 (Wed, 09 Oct 2013).

Package 346/671HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.18.4
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/IRanges
Last Changed Rev: 80662 / Revision: 81334
Last Changed Date: 2013-09-23 10:08:48 -0700 (Mon, 23 Sep 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: IRanges
Version: 1.18.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IRanges_1.18.4.tar.gz
StartedAt: 2013-10-08 22:51:25 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:57:30 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 364.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 3

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '1.18.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'IRanges' can be installed ... [45s/47s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... WARNING
Found .Internal calls in the following functions:
  'isNotSorted' 'isNotStrictlySorted'
with calls to .Internal functions
  'is.unsorted'

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'as.list.CompressedList' 'as.list.CompressedNormalIRangesList'
  'as.list.Hits' 'as.list.List' 'as.list.Rle' 'as.list.SimpleList'
  'duplicated.AtomicList' 'duplicated.CompressedAtomicList'
  'duplicated.DataTable' 'duplicated.Dups' 'duplicated.Ranges'
  'duplicated.Rle' 'duplicated.XRawList' 'levels.OverlapEncodings'
  'levels.Rle' 'sort.Rle' 'sort.RleList' 'sort.Vector' 'splitAsList'
  'splitAsListReturnedClass' 'subsetByRanges'
  'unique.CompressedAtomicList' 'unique.CompressedRleList'
  'unique.DataTable' 'unique.Rle' 'unique.SimpleRleList'
  'unique.Vector' 'window.DataTable' 'window.GappedRanges'
  'window.GroupedIRanges' 'window.IRanges' 'window.NULL' 'window.Rle'
  'window.Vector' 'window.XVector' 'window.XVectorList' 'window.factor'
  'window.vector' 'window<-.DataTable' 'window<-.RangedData'
  'window<-.Vector' 'window<-.factor' 'window<-.vector'
Undocumented S4 methods:
  generic '<=' and siglist 'XRawList,XRawList'
  generic '==' and siglist 'XRawList,XRawList'
  generic 'Ops' and siglist 'SimpleAtomicList,atomic'
  generic 'Ops' and siglist 'atomic,SimpleAtomicList'
  generic '[[<-' and siglist 'SharedRaw_Pool'
  generic 'coerce' and siglist 'ANY,DataFrame'
  generic 'compare' and siglist 'XRawList,XRawList'
  generic 'duplicated' and siglist 'CompressedAtomicList'
  generic 'duplicated' and siglist 'Rle'
  generic 'duplicated' and siglist 'XRawList'
  generic 'elementLengths' and siglist 'XVectorList'
  generic 'is.unsorted' and siglist 'XRawList'
  generic 'match' and siglist 'XRawList,XRawList'
  generic 'mstack' and siglist 'DataFrame'
  generic 'order' and siglist 'XRawList'
  generic 'rank' and siglist 'XRawList'
  generic 'relist' and siglist 'ANY,PartitioningByEnd'
  generic 'relist' and siglist 'Vector,list'
  generic 'splitAsListReturnedClass' and siglist 'ANY'
  generic 'splitAsListReturnedClass' and siglist 'DataFrame'
  generic 'splitAsListReturnedClass' and siglist 'Hits'
  generic 'splitAsListReturnedClass' and siglist 'data.frame'
  generic 'subsetByRanges' and siglist 'ANY'
  generic 'subsetByRanges' and siglist 'IRanges'
  generic 'subsetByRanges' and siglist 'NULL'
  generic 'subsetByRanges' and siglist 'vector'
  generic 'unique' and siglist 'CompressedAtomicList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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 compiled code ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/IRanges/libs/IRanges.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Object: 'errabort.o'
  Found '___stdoutp', possibly from 'stdout' (C)
    Objects: 'IntervalTree.o', 'common.o', 'errabort.o'
  Found '_abort', possibly from 'abort' (C)
    Object: 'errabort.o'
  Found '_exit', possibly from 'exit' (C)
    Object: 'errabort.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [29s/29s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'IRanges_unit_tests.R' [69s/70s]
 [70s/70s] 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

WARNING: There were 3 warnings.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/00check.log'
for details.

IRanges.Rcheck/00install.out:

* installing *source* package 'IRanges' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c AEbufs.c -o AEbufs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c CompressedList_class.c -o CompressedList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c DataFrame_class.c -o DataFrame_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c GappedRanges_class.c -o GappedRanges_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Grouping_class.c -o Grouping_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Hits_class.c -o Hits_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c IRanges_class.c -o IRanges_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c IntervalTree.c -o IntervalTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c RangedData_class.c -o RangedData_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Ranges_comparison.c -o Ranges_comparison.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c RleViews_utils.c -o RleViews_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Rle_class.c -o Rle_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function 'Rle_integer_runq':
Rle_utils.c:735: warning: implicit declaration of function 'roundingScale'
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SEXP_utils.c -o SEXP_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SharedDouble_class.c -o SharedDouble_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SharedInteger_class.c -o SharedInteger_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SharedRaw_class.c -o SharedRaw_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SharedVector_class.c -o SharedVector_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SimpleList_class.c -o SimpleList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c SimpleRangesList_class.c -o SimpleRangesList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Vector_class.c -o Vector_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c XDoubleViews_utils.c -o XDoubleViews_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c XIntegerViews_utils.c -o XIntegerViews_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c XRawList_comparison.c -o XRawList_comparison.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c XVectorList_class.c -o XVectorList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c XVector_class.c -o XVector_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c anyMissing.c -o anyMissing.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c common.c -o common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c compact_bitvector.c -o compact_bitvector.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c coverage_methods.c -o coverage_methods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c dlist.c -o dlist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c errabort.c -o errabort.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c hash_utils.c -o hash_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c int_utils.c -o int_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c inter_range_methods.c -o inter_range_methods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c localmem.c -o localmem.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c memalloc.c -o memalloc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c rbTree.c -o rbTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c safe_arithm.c -o safe_arithm.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c sort_utils.c -o sort_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c str_utils.c -o str_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c ucsc_handlers.c -o ucsc_handlers.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c vector_copy.c -o vector_copy.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o IRanges.so 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 Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XRawList_comparison.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o encodeOverlaps_methods.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 vector_copy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
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 generic function for 'subset' from package 'base' in package 'IRanges'
Creating a generic function for '%in%' from package 'base' in package 'IRanges'
in method for 'coerce' with signature '"Vector","double"': no definition for class "double"
Creating a generic function for 'append' from package 'base' in package 'IRanges'
Creating a generic function for 'relist' from package 'utils' in package 'IRanges'
in method for 'relist' with signature '"ANY","PartitioningByEnd"': no definition for class "PartitioningByEnd"
in method for 'relist' with signature '"ANY","List"': no definition for class "List"
Creating a generic function for 'split' from package 'base' in package 'IRanges'
Creating a generic function for 'split<-' from package 'base' in package 'IRanges'
Creating a generic function for 'aggregate' from package 'stats' in package 'IRanges'
Creating a generic function for 'as.list' from package 'base' in package 'IRanges'
Creating a generic function for 'unsplit' from package 'base' in package 'IRanges'
Creating a generic function for 'stack' from package 'utils' in package 'IRanges'
Creating a generic function for 'with' from package 'base' 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.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 '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 '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 generic function for 'levels' from package 'base' in package 'IRanges'
Creating a generic function for 'drop' 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'
in method for 'coerce' with signature '"xtabs","DataFrame"': no definition for class "xtabs"
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
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.9260.0230.954
DataFrame-class0.7960.0170.817
DataTable-API0.0130.0020.016
DataTable-stats0.0300.0010.031
FilterRules-class0.0970.0040.102
GappedRanges-class0.3260.0050.332
Grouping-class0.3610.0120.376
Hits-class0.1140.0030.117
IRanges-class4.0100.1584.340
IRanges-constructor0.0870.0300.126
IRanges-utils2.7620.1632.960
IRangesList-class0.0960.0180.114
IntervalTree-class0.1010.0110.114
List-class0.0150.0100.024
MaskCollection-class0.2140.0320.247
OverlapEncodings-class0.0970.0170.115
RDApplyParams-class1.8170.0351.872
RangedData-class3.0670.0753.176
RangedDataList-class0.1030.0070.111
RangedSelection-class0.0500.0070.057
Ranges-class0.1010.0370.138
Ranges-comparison0.1250.0440.170
RangesList-class0.1410.0310.173
Rle-class0.3070.0560.363
RleViews-class0.0810.0180.099
RleViewsList-class0.1130.0180.131
SimpleList-class0.0150.0090.024
Vector-class0.0180.0200.037
Views-class0.6360.0250.662
Views-utils0.1110.0230.134
ViewsList-class0.0070.0100.018
XDoubleViews-class0.1300.0220.153
XIntegerViews-class0.0950.0180.116
XVector-class0.1180.0340.153
classNameForDisplay-methods0.0270.0050.033
compact-methods0.6460.0360.700
coverage-methods0.1700.0230.197
encodeOverlaps-methods0.0530.0180.071
endoapply0.0170.0060.023
expand-methods0.3910.0130.408
findOverlaps-methods0.4700.0490.526
funprog-methods0.2070.0120.223
inter-range-methods1.4140.0621.494
intra-range-methods0.5900.0610.661
isConstant0.0140.0170.058
multisplit0.0520.0030.055
nearest-methods0.0970.0190.116
read.Mask0.0920.0340.128
reverse-methods0.1190.0130.133
runstat0.1100.0150.125
seqapply0.1310.0090.139
setops-methods0.4200.0260.448
strutils0.0060.0090.015