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Package 247/479HostnameOS / ArchBUILDCHECKBUILD BIN
IRanges 1.11.11
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges
Last Changed Rev: 56456 / Revision: 56603
Last Changed Date: 2011-06-28 16:33:41 -0700 (Tue, 28 Jun 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 (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: IRanges
Version: 1.11.11
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_1.11.11.tar.gz
StartedAt: 2011-07-07 01:05:19 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:08:28 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 188.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 4

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘1.11.11’
* 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 ... WARNING
unlist:
  function(x, recursive, use.names)
unlist.list.of.XVectorList:
  function(classname, x)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'ranges':
  ‘RangedData-class.Rd’ ‘Views-class.Rd’
Rd files with duplicated alias 'ranges<-':
  ‘RangedData-class.Rd’ ‘Views-class.Rd’
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00_pkg_src/IRanges/man/MaskCollection-class.Rd’:
  ‘[Biostrings]{reverse}’

Missing link(s) in documentation object ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00_pkg_src/IRanges/man/RleViewsList-class.Rd’:
  ‘ViewsList-class’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘AsIs’ ‘SimpleViewsList’ ‘ViewsList’
Undocumented S4 methods:
  generic '!=' and siglist 'XVector,XVector'
  generic '[' and siglist 'Views'
  generic 'as.data.frame' and siglist 'Vector'
  generic 'as.matrix' and siglist 'Views'
  generic 'coerce' and siglist 'Vector,data.frame'
  generic 'coerce' and siglist 'Views,IRanges'
  generic 'coerce' and siglist 'Views,Ranges'
  generic 'elementLengths' and siglist 'Views'
  generic 'end' and siglist 'SimpleViewsList'
  generic 'end' and siglist 'Views'
  generic 'end<-' and siglist 'Views'
  generic 'length' and siglist 'Views'
  generic 'names' and siglist 'Views'
  generic 'names<-' and siglist 'Views'
  generic 'narrow' and siglist 'Views'
  generic 'ranges' and siglist 'SimpleViewsList'
  generic 'reduce' and siglist 'Views'
  generic 'shift' and siglist 'Views'
  generic 'slice' and siglist 'numeric'
  generic 'start' and siglist 'SimpleViewsList'
  generic 'start' and siglist 'Views'
  generic 'start<-' and siglist 'Views'
  generic 'unique' and siglist 'Vector'
  generic 'universe' and siglist 'ViewsList'
  generic 'universe<-' and siglist 'ViewsList'
  generic 'width' and siglist 'SimpleViewsList'
  generic 'width' and siglist 'Views'
  generic 'width<-' and siglist 'Views'
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 ... 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

WARNING: There were 4 warnings, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/00check.log’
for details

IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
Ocopy_byteblocks.c: In function ‘translate_byte’:
Ocopy_byteblocks.c:20:16: warning: ‘lkup_val’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rle_utils.c -o Rle_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XDoubleViews_utils.c -o XDoubleViews_utils.o
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 ‘get_cachedDoubleSeq_which_min’:
XDoubleViews_utils.c:185:9: warning: ‘cur_min’ 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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c common.c -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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 -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c dlist.c -o dlist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c errabort.c -o errabort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c localmem.c -o localmem.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c memalloc.c -o memalloc.o
memalloc.c: In function ‘carefulAlloc’:
memalloc.c:293:2: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘size_t’
memalloc.c:293:2: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
memalloc.c:289:10: warning: unused variable ‘allocRequest’
memalloc.c:288:10: warning: unused variable ‘maxAlloc’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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_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 -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/IRanges.Rcheck/IRanges/libs
** 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

* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.4920.0040.496
DataFrame-class0.6040.0000.603
DataTable-API0.0040.0000.001
DataTable-stats0.0120.0000.013
FilterRules-class0.0360.0000.036
GappedRanges-class0.1800.0000.182
Grouping-class0.10.00.1
IRanges-class1.6560.2721.929
IRanges-constructor0.0560.0000.058
IRanges-setops0.1480.0000.148
IRanges-utils1.7040.2602.005
IRangesList-class0.0440.0000.046
IntervalTree-class0.1640.0040.165
List-class0.0040.0000.006
MaskCollection-class0.1840.0000.187
RDApplyParams-class0.6840.0000.686
RangedData-class1.5920.0041.625
RangedData-utils0.0920.0000.091
RangedDataList-class0.0400.0000.041
RangedSelection-class0.0240.0000.023
Ranges-class0.0720.0000.077
Ranges-comparison0.0320.0000.032
Ranges-utils0.1360.0000.133
RangesList-class0.1760.0000.194
RangesList-utils0.4600.0120.483
RangesMatching-class0.0160.0000.012
Rle-class0.1160.0000.115
RleViews-class0.0600.0000.061
RleViewsList-class0.0640.0000.063
SimpleList-class0.0080.0000.006
Vector-class0.0040.0000.006
Views-class0.3240.0040.330
Views-utils0.0520.0080.060
XDoubleViews-class0.0600.0000.064
XIntegerViews-class0.0440.0040.050
XVector-class0.0400.0000.044
compact0.4600.0080.468
coverage0.0800.0000.082
disjoin0.0160.0000.016
endoapply0.0120.0000.010
isConstant0.0040.0000.003
nearest0.0320.0000.032
read.Mask0.060.000.06
reverse0.0680.0040.070
runstat0.0320.0000.031
seqapply0.0640.0000.063
strutils0.0000.0000.001