BioC 2.12: CHECK report for MineICA on petty

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: 2013-10-08 23:04:09 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:13:15 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 546.6 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 3.0.1 (2013-05-16)
* 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 ... [40s/42s] 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 ... [45s/83s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
annotFeaturesComp 3.865   0.09   7.412
* 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	1.238	0.058	2.359
annotFeaturesComp	3.865	0.090	7.412
annotFeaturesWithBiomaRt	0.027	0.008	0.082
annotInGene	1.811	0.044	3.101
annotReciprocal	0.027	0.003	0.037
buildIcaSet	0.793	0.056	1.481
buildMineICAParams	0.029	0.029	0.126
class-IcaSet	1.409	0.036	3.058
class-MineICAParams	0.052	0.012	0.138
clusVarAnalysis	0.349	0.042	0.646
clusterFastICARuns	0.377	0.015	0.650
clusterSamplesByComp	2.020	0.039	3.313
clusterSamplesByComp_multiple	0.570	0.034	1.120
compareAn	1.742	0.043	2.984
compareAn2graphfile	1.331	0.037	2.200
compareGenes	0.025	0.003	0.031
cor2An	0.062	0.011	0.123
getProj	0.082	0.016	0.137
getSdExpr	0.018	0.005	0.026
hypergeoAn	0.036	0.006	0.078
nbOccByGeneInComp	0.046	0.006	0.073
nbOccInComp	0.297	0.030	0.526
nbOccInComp_simple	0.103	0.032	0.220
nodeAttrs	0.021	0.003	0.026
plotAllMix	1.289	0.015	2.245
plotCorGraph	2.204	0.090	4.312
plotDensAllAnnotInAllComp	0.029	0.004	0.054
plotDensOneAnnotInAllComp	0.458	0.006	0.759
plotMclust	0.185	0.005	0.292
plotMix	0.185	0.006	0.288
plotPosAnnotInComp	0.035	0.006	0.065
plotPosSamplesInComp	0.034	0.007	0.082
plot_heatmapsOnSel	0.032	0.010	0.068
qualVarAnalysis	0.284	0.039	0.517
quantVarAnalysis	0.381	0.050	0.648
relativePath	0.016	0.003	0.030
runAn	0.035	0.006	0.070
runCompareIcaSets	1.403	0.026	2.108
runEnrich	0.021	0.004	0.035
runICA	0.245	0.008	0.391
selectContrib	0.045	0.007	0.083
selectFeatures_IQR	0.309	0.028	0.463
selectWitnessGenes	0.302	0.038	0.396
writeGenes	0.046	0.003	0.064
writeGostatsHtmltable	0.039	0.006	0.059
writeProjByComp	0.045	0.008	0.087