Package: KCsmart

Version: 2.14.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings KCsmart_2.14.0.tar.gz

StartedAt: 2012-04-01 01:49:58 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:51:40 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 102.5 seconds

RetCode: 0

Status:  OK

CheckDir: KCsmart.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/KCsmart.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.14.0'
* 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 whether package 'KCsmart' 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 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 ... NOTE
prepare_Rd: calcSpm.Rd:52-53: Dropping empty section \note
prepare_Rd: calcSpm.Rd:50: Dropping empty section \references
prepare_Rd: calcSpmCollection.Rd:54-55: Dropping empty section \note
prepare_Rd: calcSpmCollection.Rd:52: 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:79-81: Dropping empty section \value
prepare_Rd: write.table.Rd:83-84: 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 for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/KCsmart.Rcheck/00check.log'
for details.

* installing *source* package 'KCsmart' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'sort' from package 'base' in package 'KCsmart'
Creating a generic function for 'unlist' from package 'base' in package 'KCsmart'
Creating a generic function for 'write.table' from package 'utils' in package 'KCsmart'
** help
*** installing help indices
** building package indices
** installing vignettes
   'KCS.Rnw' 
** testing if installed package can be loaded

* DONE (KCsmart)

name	user	system	elapsed
KCsmart-package	18.245	0.212	18.482
calcSpm	1.340	0.012	1.365
calcSpmCollection	9.052	0.068	9.147
compKc-class	0.000	0.000	0.001
compKcSigRegions-class	0.000	0.000	0.001
compareSpmCollection	8.781	0.028	8.836
findSigLevelFdr	2.500	0.020	2.573
findSigLevelTrad	1.956	0.020	1.993
getSigRegionsCompKC	9.293	0.064	9.382
getSigSegments	1.476	0.004	1.503
idPoints	0.008	0.000	0.027
plot	2.388	0.016	2.422
plotScaleSpace	3.600	0.004	3.620
samplePointMatrix-class	0.000	0.000	0.001
sigSegments-class	0.004	0.000	0.000
spmCollection-class	0.000	0.000	0.001
write.table	1.700	0.000	1.715