BioC 2.14: CHECK report for MineICA on moscato2

Package: MineICA

Version: 1.4.0

Command: rm -rf MineICA.buildbin-libdir && mkdir MineICA.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MineICA.buildbin-libdir MineICA_1.4.0.tar.gz >MineICA-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MineICA.buildbin-libdir --install="check:MineICA-install.out" --force-multiarch --no-vignettes --timings MineICA_1.4.0.tar.gz

StartedAt: 2014-10-08 02:55:25 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 03:02:34 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 429.1 seconds

RetCode: 0

Status:  OK

CheckDir: MineICA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MineICA.buildbin-libdir && mkdir MineICA.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MineICA.buildbin-libdir MineICA_1.4.0.tar.gz >MineICA-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=MineICA.buildbin-libdir --install="check:MineICA-install.out" --force-multiarch --no-vignettes --timings MineICA_1.4.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/MineICA.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MineICA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MineICA' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'

Depends: includes the non-default packages:
  'Biobase' 'plyr' 'ggplot2' 'scales' 'foreach' 'xtable' 'biomaRt'
  'gtools' 'GOstats' 'cluster' 'marray' 'mclust' 'RColorBrewer'
  'colorspace' 'igraph' 'Rgraphviz' 'graph' 'annotate' 'Hmisc'
  'fastICA' 'JADE'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'MineICA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'biomaRt' 'GOstats' 'cluster' 'mclust' 'igraph'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GOstats' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'lumiHumanAll.db'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GOstats' 'Hmisc' 'JADE' 'RColorBrewer' 'Rgraphviz' 'annotate'
  'biomaRt' 'cluster' 'colorspace' 'fastICA' 'foreach' 'ggplot2'
  'graph' 'gtools' 'igraph' 'marray' 'mclust' 'methods' 'plyr' 'scales'
  'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'Biobase:::annotation' 'Biobase:::validMsg' 'fpc:::pamk'
  'lumi:::getChipInfo' 'mclust:::adjustedRandIndex'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::isValidVersion'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [33s] OK
** running examples for arch 'x64' ... [36s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/MineICA.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MineICA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MineICA' as MineICA_1.4.0.zip
* DONE (MineICA)

name	user	system	elapsed
annotFeatures	0.41	0.03	0.43
annotFeaturesComp	2.34	0.00	2.38
annotFeaturesWithBiomaRt	0.02	0.00	0.02
annotInGene	1.10	0.00	1.11
annotReciprocal	0.02	0.00	0.01
buildIcaSet	0.44	0.02	0.69
buildMineICAParams	0.00	0.00	0.47
class-IcaSet	0.53	0.04	1.59
class-MineICAParams	0.01	0.00	0.01
clusVarAnalysis	0.13	0.00	0.38
clusterFastICARuns	0.15	0.00	0.16
clusterSamplesByComp	2.77	0.02	3.01
clusterSamplesByComp_multiple	0.31	0.00	0.53
compareAn	0.75	0.01	0.99
compareAn2graphfile	0.54	0.02	0.77
compareGenes	0	0	0
cor2An	0.01	0.00	0.02
getProj	0.03	0.01	0.05
getSdExpr	0	0	0
hypergeoAn	0	0	0
nbOccByGeneInComp	0.02	0.02	0.03
nbOccInComp	0.22	0.00	0.45
nbOccInComp_simple	0.05	0.00	0.28
nodeAttrs	0.01	0.00	0.02
plotAllMix	1.72	0.00	1.71
plotCorGraph	1.71	0.00	1.95
plotDensAllAnnotInAllComp	0	0	0
plotDensOneAnnotInAllComp	0	0	0
plotMclust	0.21	0.00	0.21
plotMix	0.2	0.0	0.2
plotPosAnnotInComp	0	0	0
plotPosSamplesInComp	0	0	0
plot_heatmapsOnSel	0	0	0
qualVarAnalysis	0.19	0.00	0.43
quantVarAnalysis	0.50	0.03	0.78
relativePath	0	0	0
runAn	0	0	0
runCompareIcaSets	0.56	0.00	0.80
runEnrich	0	0	0
runICA	0.09	0.00	0.09
selectContrib	0	0	0
selectFeatures_IQR	0.16	0.00	0.16
selectWitnessGenes	0.12	0.02	0.37
writeGenes	0	0	0
writeGostatsHtmltable	0.02	0.00	0.02
writeProjByComp	0	0	0

name	user	system	elapsed
annotFeatures	0.5	0.0	0.5
annotFeaturesComp	2.70	0.01	2.77
annotFeaturesWithBiomaRt	0	0	0
annotInGene	1.21	0.02	1.25
annotReciprocal	0.02	0.00	0.01
buildIcaSet	0.36	0.03	0.61
buildMineICAParams	0.00	0.00	0.47
class-IcaSet	0.61	0.08	2.00
class-MineICAParams	0	0	0
clusVarAnalysis	0.10	0.00	0.36
clusterFastICARuns	0.18	0.00	0.17
clusterSamplesByComp	2.40	0.00	2.64
clusterSamplesByComp_multiple	0.31	0.00	0.53
compareAn	0.58	0.00	0.81
compareAn2graphfile	0.70	0.00	0.94
compareGenes	0.02	0.00	0.01
cor2An	0.03	0.02	0.05
getProj	0.06	0.00	0.06
getSdExpr	0	0	0
hypergeoAn	0	0	0
nbOccByGeneInComp	0.03	0.00	0.03
nbOccInComp	0.34	0.00	0.58
nbOccInComp_simple	0.08	0.00	0.31
nodeAttrs	0.01	0.00	0.02
plotAllMix	1.56	0.00	1.56
plotCorGraph	1.99	0.01	2.21
plotDensAllAnnotInAllComp	0.01	0.00	0.02
plotDensOneAnnotInAllComp	0	0	0
plotMclust	0.19	0.00	0.18
plotMix	0.19	0.00	0.19
plotPosAnnotInComp	0	0	0
plotPosSamplesInComp	0	0	0
plot_heatmapsOnSel	0	0	0
qualVarAnalysis	0.21	0.00	0.47
quantVarAnalysis	0.28	0.02	0.64
relativePath	0	0	0
runAn	0	0	0
runCompareIcaSets	1.61	0.03	1.84
runEnrich	0	0	0
runICA	0.19	0.00	0.19
selectContrib	0.01	0.00	0.01
selectFeatures_IQR	0.28	0.00	0.28
selectWitnessGenes	0.24	0.00	0.52
writeGenes	0.01	0.00	0.01
writeGostatsHtmltable	0.02	0.00	0.02
writeProjByComp	0	0	0