Package: MineICA

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MineICA_0.99.1.tar.gz

StartedAt: 2013-03-24 07:40:49 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 07:47:07 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 378.4 seconds

RetCode: 0

Status:  OK

CheckDir: MineICA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MineICA.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MineICA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MineICA' version '0.99.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'MineICA' can be installed ... [35s/36s] 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 ... NOTE
plotPosOneAnnotLevInComp_ggplot: no visible binding for global variable
  '..count..'
plotPosSamplesInComp_ggplot: no visible binding for global variable
  '..count..'
* checking Rd files ... OK
* 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 ... [38s/39s] 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/MineICA.Rcheck/00check.log'
for details.

* installing *source* package 'MineICA' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'sampleNames<-' in package 'MineICA'
** help
*** installing help indices
** building package indices
** installing vignettes
   'MineICA.Rnw' 
** testing if installed package can be loaded
* DONE (MineICA)

name	user	system	elapsed
annotFeatures	0.669	0.055	0.746
annotFeaturesComp	3.133	0.068	3.236
annotFeaturesWithBiomaRt	0.028	0.008	0.036
annotInGene	1.670	0.036	1.711
annotReciprocal	0.024	0.003	0.028
buildIcaSet	0.653	0.047	0.706
buildMineICAParams	0.038	0.026	0.067
class-IcaSet	1.038	0.034	1.872
class-MineICAParams	0.055	0.006	0.062
clusVarAnalysis	0.215	0.036	0.256
clusterFastICARuns	0.265	0.012	0.279
clusterSamplesByComp	1.866	0.035	1.916
clusterSamplesByComp_multiple	0.542	0.029	0.576
compareAn	1.123	0.038	1.176
compareAn2graphfile	0.998	0.038	1.039
compareGenes	0.025	0.003	0.028
cor2An	0.564	0.012	0.577
getProj	0.067	0.019	0.085
getSdExpr	0.016	0.004	0.019
hypergeoAn	0.028	0.009	0.038
nbOccByGeneInComp	0.056	0.008	0.063
nbOccInComp	0.246	0.029	0.278
nbOccInComp_simple	0.103	0.033	0.139
nodeAttrs	0.015	0.004	0.019
plotAllMix	1.099	0.014	1.119
plotCorGraph	1.912	0.046	2.149
plotDensAllAnnotInAllComp	0.014	0.004	0.019
plotDensOneAnnotInAllComp	0.026	0.005	0.032
plotMclust	0.179	0.005	0.184
plotMix	0.187	0.004	0.191
plotPosAnnotInComp	0.041	0.006	0.047
plotPosSamplesInComp	0.053	0.005	0.058
plot_heatmapsOnSel	0.051	0.007	0.057
qualVarAnalysis	0.252	0.042	0.297
quantVarAnalysis	0.341	0.047	0.410
relativePath	0.032	0.003	0.067
runAn	0.028	0.006	0.034
runCompareIcaSets	1.113	0.039	1.156
runEnrich	0.049	0.005	0.054
runICA	0.649	0.006	0.656
selectContrib	0.048	0.012	0.061
selectFeatures_IQR	0.226	0.033	0.259
selectWitnessGenes	0.224	0.037	0.281
writeGenes	0.034	0.010	0.044
writeGostatsHtmltable	0.045	0.009	0.055
writeProjByComp	0.043	0.009	0.052