BioC 2.12: CHECK report for MineICA on george2

Package: MineICA

Version: 1.0.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MineICA_1.0.0.tar.gz

StartedAt: 2013-10-09 03:15:17 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:23:12 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 475.1 seconds

RetCode: 0

Status:  OK

CheckDir: MineICA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/MineICA.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [45s/46s] 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 ... [51s/53s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
annotFeaturesComp 5.132  0.112   5.256
* 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
  ‘/home/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	0.668	0.020	0.700
annotFeaturesComp	5.132	0.112	5.256
annotFeaturesWithBiomaRt	0.032	0.008	0.039
annotInGene	2.452	0.108	2.566
annotReciprocal	0.036	0.000	0.033
buildIcaSet	0.708	0.140	0.855
buildMineICAParams	0.056	0.228	0.295
class-IcaSet	1.288	0.032	2.327
class-MineICAParams	0.112	0.000	0.113
clusVarAnalysis	1.020	0.216	1.249
clusterFastICARuns	0.356	0.000	0.355
clusterSamplesByComp	2.589	0.112	2.712
clusterSamplesByComp_multiple	0.444	0.120	0.570
compareAn	1.224	0.132	1.675
compareAn2graphfile	1.288	0.116	1.495
compareGenes	0.044	0.000	0.045
cor2An	0.072	0.004	0.077
getProj	0.796	0.052	0.847
getSdExpr	0.024	0.004	0.028
hypergeoAn	0.056	0.000	0.054
nbOccByGeneInComp	0.096	0.004	0.098
nbOccInComp	0.252	0.112	0.376
nbOccInComp_simple	0.096	0.116	0.222
nodeAttrs	0.048	0.004	0.052
plotAllMix	1.524	0.012	1.544
plotCorGraph	1.632	0.168	1.845
plotDensAllAnnotInAllComp	0.796	0.020	0.817
plotDensOneAnnotInAllComp	0.072	0.004	0.078
plotMclust	0.244	0.000	0.247
plotMix	0.232	0.000	0.232
plotPosAnnotInComp	0.048	0.000	0.049
plotPosSamplesInComp	0.072	0.000	0.074
plot_heatmapsOnSel	0.116	0.000	0.112
qualVarAnalysis	0.288	0.164	0.483
quantVarAnalysis	0.356	0.260	0.782
relativePath	0.024	0.004	0.031
runAn	0.032	0.000	0.031
runCompareIcaSets	1.304	0.140	1.560
runEnrich	0.064	0.000	0.062
runICA	0.224	0.004	0.227
selectContrib	0.112	0.000	0.112
selectFeatures_IQR	0.208	0.004	0.213
selectWitnessGenes	0.384	0.120	0.513
writeGenes	0.140	0.000	0.139
writeGostatsHtmltable	0.044	0.004	0.046
writeProjByComp	0.076	0.004	0.081