BioC 2.11: CHECK report for KCsmart on perceval

Package: KCsmart

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KCsmart_2.16.0.tar.gz

StartedAt: 2013-03-25 00:10:48 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:14:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 221.7 seconds

RetCode: 0

Status: OK

CheckDir: KCsmart.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/KCsmart.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.16.0'
* 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 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 ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      28.302 11.276  40.920
getSigRegionsCompKC  15.592  8.903  27.481
compareSpmCollection 15.071  8.905  25.580
calcSpmCollection    15.007  8.538  25.422
plotScaleSpace        7.063  3.891  11.516
plot                  4.122  1.798   6.224
findSigLevelFdr       3.992  1.797   6.203
write.table           3.205  1.764   5.237
findSigLevelTrad      3.284  1.635   5.987
getSigSegments        2.919  1.870   5.323
* 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
  '/Users/biocbuild/bbs-2.11-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	28.302	11.276	40.920
calcSpm	2.099	0.837	3.070
calcSpmCollection	15.007	8.538	25.422
compKc-class	0.001	0.001	0.001
compKcSigRegions-class	0.000	0.000	0.001
compareSpmCollection	15.071	8.905	25.580
findSigLevelFdr	3.992	1.797	6.203
findSigLevelTrad	3.284	1.635	5.987
getSigRegionsCompKC	15.592	8.903	27.481
getSigSegments	2.919	1.870	5.323
idPoints	0.015	0.003	0.023
plot	4.122	1.798	6.224
plotScaleSpace	7.063	3.891	11.516
samplePointMatrix-class	0.001	0.000	0.001
sigSegments-class	0.000	0.000	0.002
spmCollection-class	0.001	0.001	0.001
write.table	3.205	1.764	5.237

Summary

Command output