Package: MineICA

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MineICA_1.0.0.tar.gz

StartedAt: 2013-05-01 08:00:40 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:06:59 -0700 (Wed, 01 May 2013)

EllapsedTime: 379.3 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 Patched (2013-04-08 r62531)
* 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 '1.0.0'
* 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 ... [34s/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 ... [37s/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
** testing if installed package can be loaded
* DONE (MineICA)

name	user	system	elapsed
annotFeatures	0.669	0.052	0.747
annotFeaturesComp	3.410	0.075	3.643
annotFeaturesWithBiomaRt	0.023	0.008	0.031
annotInGene	1.552	0.040	1.605
annotReciprocal	0.020	0.004	0.024
buildIcaSet	0.590	0.060	0.698
buildMineICAParams	0.035	0.021	0.061
class-IcaSet	1.407	0.040	2.362
class-MineICAParams	0.040	0.012	0.053
clusVarAnalysis	0.189	0.034	0.227
clusterFastICARuns	0.272	0.013	0.290
clusterSamplesByComp	1.873	0.033	1.919
clusterSamplesByComp_multiple	0.443	0.029	0.487
compareAn	0.973	0.030	1.022
compareAn2graphfile	0.953	0.046	1.026
compareGenes	0.021	0.006	0.027
cor2An	0.043	0.011	0.054
getProj	0.062	0.013	0.075
getSdExpr	0.022	0.003	0.025
hypergeoAn	0.032	0.006	0.039
nbOccByGeneInComp	0.054	0.007	0.061
nbOccInComp	0.599	0.028	0.639
nbOccInComp_simple	0.071	0.019	0.091
nodeAttrs	0.015	0.005	0.020
plotAllMix	1.037	0.011	1.101
plotCorGraph	1.464	0.048	1.584
plotDensAllAnnotInAllComp	0.071	0.004	0.075
plotDensOneAnnotInAllComp	0.041	0.003	0.045
plotMclust	0.200	0.002	0.202
plotMix	0.199	0.004	0.203
plotPosAnnotInComp	0.057	0.005	0.063
plotPosSamplesInComp	0.049	0.006	0.055
plot_heatmapsOnSel	0.079	0.007	0.089
qualVarAnalysis	0.255	0.032	0.292
quantVarAnalysis	0.291	0.042	0.355
relativePath	0.015	0.004	0.018
runAn	0.028	0.007	0.035
runCompareIcaSets	0.973	0.025	1.012
runEnrich	0.027	0.003	0.030
runICA	0.205	0.006	0.215
selectContrib	0.049	0.011	0.061
selectFeatures_IQR	0.205	0.030	0.236
selectWitnessGenes	0.249	0.023	0.272
writeGenes	0.033	0.008	0.041
writeGostatsHtmltable	0.053	0.007	0.059
writeProjByComp	0.032	0.009	0.040