Package: KCsmart

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings KCsmart_2.6.0.tar.gz

StartedAt: 2010-10-04 17:32:31 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:44:08 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 697.3 seconds

RetCode: 0

Status:  OK

CheckDir: KCsmart.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/KCsmart.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'KCsmart' can be installed ... 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 ... NOTE
prepare_Rd: calcSpm.Rd:49-50: Dropping empty section \note
prepare_Rd: calcSpm.Rd:47: Dropping empty section \references
prepare_Rd: calcSpmCollection.Rd:51-52: Dropping empty section \note
prepare_Rd: calcSpmCollection.Rd:49: Dropping empty section \references
prepare_Rd: compareSpmCollection.Rd:28-29: Dropping empty section \note
prepare_Rd: compareSpmCollection.Rd:26: Dropping empty section \references
prepare_Rd: getSigRegionsCompKC.Rd:30-31: Dropping empty section \note
prepare_Rd: getSigRegionsCompKC.Rd:28: Dropping empty section \references
prepare_Rd: getSigSegments.Rd:29-30: Dropping empty section \note
prepare_Rd: hsSampleData.Rd:12-13: Dropping empty section \references
prepare_Rd: idPoints.Rd:29-30: Dropping empty section \note
prepare_Rd: plot.Rd:39-40: Dropping empty section \details
prepare_Rd: plot.Rd:51-52: Dropping empty section \note
prepare_Rd: plotScaleSpace.Rd:25-26: Dropping empty section \note
prepare_Rd: write.table.Rd:73-75: Dropping empty section \value
prepare_Rd: write.table.Rd:77-78: Dropping empty section \note
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package ‘KCsmart’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: multtest
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: splines
Creating a new generic function for "sort" in "KCsmart"
Creating a new generic function for "unlist" in "KCsmart"
Creating a new generic function for "write.table" in "KCsmart"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (KCsmart)

name	user	system	elapsed
KCsmart-package	103.436	43.564	150.378
calcSpm	7.517	3.160	10.852
calcSpmCollection	70.160	30.177	103.909
compKc-class	0.002	0.000	0.002
compKcSigRegions-class	0.001	0.000	0.002
compareSpmCollection	74.112	33.150	111.341
findSigLevelFdr	15.211	6.834	25.203
findSigLevelTrad	15.787	6.799	23.223
getSigRegionsCompKC	71.941	31.321	107.471
getSigSegments	15.051	6.083	21.484
idPoints	0.040	0.004	0.044
plot	15.663	6.197	22.923
plotScaleSpace	32.646	13.375	47.291
samplePointMatrix-class	0.002	0.001	0.002
sigSegments-class	0.001	0.000	0.001
spmCollection-class	0.002	0.000	0.006
write.table	14.664	6.095	22.428