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: 2013-03-25 03:33:12 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:38:42 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 329.9 seconds

RetCode: 0

Status:  OK

CheckDir: MineICA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MineICA.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [29s/30s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [32s/33s] 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	0.578	0.067	0.647
annotFeaturesComp	1.766	0.137	1.905
annotFeaturesWithBiomaRt	0.019	0.009	0.029
annotInGene	1.116	0.153	1.317
annotReciprocal	0.018	0.007	0.024
buildIcaSet	0.633	0.142	0.782
buildMineICAParams	0.028	0.095	0.128
class-IcaSet	0.864	0.088	1.736
class-MineICAParams	0.029	0.019	0.049
clusVarAnalysis	0.206	0.117	0.325
clusterFastICARuns	0.515	0.139	0.666
clusterSamplesByComp	1.657	0.109	1.769
clusterSamplesByComp_multiple	0.385	0.120	0.509
compareAn	1.016	0.156	1.180
compareAn2graphfile	0.831	0.145	0.980
compareGenes	0.012	0.007	0.020
cor2An	0.038	0.015	0.054
getProj	0.059	0.014	0.074
getSdExpr	0.014	0.006	0.020
hypergeoAn	0.019	0.011	0.031
nbOccByGeneInComp	0.037	0.009	0.046
nbOccInComp	0.204	0.085	0.294
nbOccInComp_simple	0.084	0.083	0.172
nodeAttrs	0.017	0.008	0.026
plotAllMix	0.926	0.035	0.968
plotCorGraph	1.599	0.249	1.887
plotDensAllAnnotInAllComp	0.033	0.011	0.044
plotDensOneAnnotInAllComp	0.034	0.011	0.045
plotMclust	0.202	0.013	0.218
plotMix	0.174	0.009	0.184
plotPosAnnotInComp	0.010	0.008	0.018
plotPosSamplesInComp	0.024	0.012	0.043
plot_heatmapsOnSel	0.022	0.013	0.036
qualVarAnalysis	0.190	0.126	0.318
quantVarAnalysis	0.288	0.197	0.488
relativePath	0.023	0.009	0.031
runAn	0.022	0.012	0.036
runCompareIcaSets	1.216	0.177	1.400
runEnrich	0.016	0.008	0.025
runICA	0.155	0.016	0.171
selectContrib	0.044	0.018	0.068
selectFeatures_IQR	0.195	0.033	0.229
selectWitnessGenes	0.282	0.095	0.378
writeGenes	0.034	0.013	0.047
writeGostatsHtmltable	0.038	0.012	0.049
writeProjByComp	0.030	0.016	0.046