Package: MineICA

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MineICA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MineICA_1.20.0.tar.gz

StartedAt: 2018-10-16 22:38:45 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:42:37 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 231.6 seconds

RetCode: 0

Status:  OK

CheckDir: MineICA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MineICA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MineICA_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MineICA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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:
  ‘BiocGenerics’ ‘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 for sufficient/correct file permissions ... 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
* 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 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGenesToGoReport: no visible global function definition for
  ‘geneIdsByCategory’
addGenesToGoReport: no visible global function definition for
  ‘geneIdUniverse’
addGenesToGoReport: no visible global function definition for
  ‘conditional’
addGenesToGoReport: no visible global function definition for
  ‘sigCategories’
annot2Color: no visible global function definition for ‘brewer.pal’
annot2Color: no visible global function definition for ‘heat_hcl’
annot2Color: no visible global function definition for ‘terrain_hcl’
annot2Color: no visible global function definition for ‘cm.colors’
annot2Color: no visible global function definition for ‘rainbow_hcl’
annotFeatures: no visible global function definition for ‘na.omit’
annotFeaturesComp: no visible global function definition for ‘getEG’
annotFeaturesComp: no visible global function definition for
  ‘getSYMBOL’
annotFeaturesComp: no visible global function definition for ‘llply’
annotFeaturesComp : <anonymous> : <anonymous>: no visible global
  function definition for ‘median’
annotFeaturesComp : <anonymous>: no visible binding for global variable
  ‘median’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘useMart’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘listFilters’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘listAttributes’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘getBM’
annotReciprocal: no visible global function definition for
  ‘write.table’
buildIcaSet: no visible global function definition for ‘new’
buildIcaSet: no visible global function definition for ‘read.table’
buildMineICAParams: no visible global function definition for ‘new’
clusVarAnalysis : <anonymous> : <anonymous>: no visible global function
  definition for ‘chisq.test’
clusVarAnalysis : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘chisq.test’
clusVarAnalysis: no visible binding for global variable ‘p.adjust’
clusVarAnalysis: no visible global function definition for ‘%do%’
clusVarAnalysis: no visible global function definition for ‘foreach’
clusVarAnalysis: no visible global function definition for ‘ggplot’
clusVarAnalysis: no visible global function definition for ‘geom_bar’
clusVarAnalysis: no visible global function definition for ‘aes’
clusVarAnalysis: no visible binding for global variable ‘cluster’
clusVarAnalysis: no visible global function definition for ‘xlab’
clusVarAnalysis: no visible global function definition for ‘ggtitle’
clusVarAnalysis: no visible global function definition for
  ‘scale_fill_manual’
clusVarAnalysis: no visible global function definition for ‘ggsave’
clusVarAnalysis: no visible global function definition for
  ‘write.table’
clusterFastICARuns: no visible global function definition for ‘fastICA’
clusterFastICARuns: no visible global function definition for ‘%dopar%’
clusterFastICARuns: no visible global function definition for ‘foreach’
clusterFastICARuns: no visible global function definition for ‘cor’
clusterFastICARuns: no visible global function definition for ‘hclust’
clusterFastICARuns: no visible global function definition for ‘as.dist’
clusterFastICARuns: no visible global function definition for ‘cutree’
clusterFastICARuns: no visible global function definition for ‘agnes’
clusterFastICARuns: no visible global function definition for
  ‘as.hclust’
clusterFastICARuns: no visible global function definition for ‘pam’
clusterFastICARuns: no visible global function definition for ‘kmeans’
clusterSamplesByComp: no visible global function definition for ‘%do%’
clusterSamplesByComp: no visible global function definition for
  ‘foreach’
clusterSamplesByComp: no visible global function definition for
  ‘Mclust’
clusterSamplesByComp: no visible global function definition for
  ‘kmeans’
clusterSamplesByComp: no visible global function definition for ‘pam’
clusterSamplesByComp: no visible global function definition for ‘dist’
clusterSamplesByComp: no visible global function definition for
  ‘hclust’
clusterSamplesByComp: no visible global function definition for
  ‘cutree’
clusterSamplesByComp: no visible global function definition for ‘agnes’
clusterSamplesByComp: no visible global function definition for
  ‘as.hclust’
clusterSamplesByComp: no visible binding for global variable ‘cluster’
clusterSamplesByComp: no visible global function definition for
  ‘write.table’
clusterSamplesByComp_multiple: no visible global function definition
  for ‘%do%’
clusterSamplesByComp_multiple: no visible global function definition
  for ‘foreach’
clusterSamplesByComp_multiple: no visible global function definition
  for ‘aggregate’
clusterSamplesByComp_multiple: no visible global function definition
  for ‘write.table’
compareAn: no visible global function definition for ‘combn’
compareAn2graphfile : <anonymous>: no visible binding for global
  variable ‘cor’
compareAn2graphfile: no visible global function definition for
  ‘write.table’
compareGenes: no visible global function definition for ‘useMart’
compareGenes: no visible global function definition for ‘%dopar%’
compareGenes: no visible global function definition for ‘foreach’
compareGenes: no visible global function definition for ‘llply’
compareGenes: no visible binding for global variable ‘median’
cor2An: no visible global function definition for ‘rcorr’
cor2An : <anonymous>: no visible global function definition for
  ‘cor.test’
cor2An: no visible global function definition for ‘cor.test’
correl2Comp: no visible global function definition for ‘cor.test’
correl2Comp: no visible global function definition for ‘cor’
doEnrichment: no visible global function definition for ‘na.omit’
doEnrichment: no visible global function definition for ‘new’
doEnrichment: no visible global function definition for ‘hyperGTest’
heatmap.plus: no visible binding for global variable ‘dist’
heatmap.plus: no visible binding for global variable ‘agnes’
heatmap.plus : <anonymous>: no visible global function definition for
  ‘reorder’
heatmap.plus: no visible global function definition for ‘as.dendrogram’
heatmap.plus: no visible global function definition for ‘as.hclust’
heatmap.plus: no visible global function definition for
  ‘order.dendrogram’
heatmap.plus: no visible global function definition for ‘par’
heatmap.plus: no visible global function definition for ‘layout’
heatmap.plus: no visible global function definition for ‘axis’
heatmap.plus: no visible global function definition for ‘quantile’
heatmap.plus: no visible global function definition for ‘heat.colors’
heatmap.plus: no visible global function definition for ‘mtext’
heatmap.plus: no visible global function definition for ‘plot’
heatmap.plus: no visible global function definition for ‘frame’
heatmap.plus: no visible global function definition for ‘title’
hypergeoAn: no visible global function definition for ‘na.omit’
hypergeoAn: no visible global function definition for ‘llply’
mergeGostatsResults: no visible global function definition for
  ‘%dopar%’
mergeGostatsResults: no visible global function definition for
  ‘foreach’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘%dopar%’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘foreach’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘xtable’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘capture.output’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘%do%’
mergeGostatsResults: no visible global function definition for ‘xtable’
mergeGostatsResults: no visible global function definition for
  ‘capture.output’
nbOccInComp: no visible global function definition for ‘read.table’
nbOccInComp: no visible global function definition for ‘aggregate’
nbOccInComp: no visible global function definition for ‘pdf’
nbOccInComp: no visible global function definition for ‘plot’
nbOccInComp: no visible global function definition for ‘dev.off’
nbOccInComp: no visible global function definition for ‘%dopar%’
nbOccInComp: no visible global function definition for ‘foreach’
nbOccInComp: no visible global function definition for ‘xtable’
nbOccInComp: no visible global function definition for ‘capture.output’
nodeAttrs: no visible global function definition for ‘%do%’
nodeAttrs: no visible global function definition for ‘foreach’
nodeAttrs: no visible global function definition for ‘write.table’
plotAllMix: no visible binding for global variable ‘Mclust’
plotAllMix: no visible global function definition for ‘par’
plotAllMix: no visible global function definition for ‘dev.off’
plotCorGraph: no visible global function definition for ‘brewer.pal’
plotCorGraph: no visible global function definition for ‘llply’
plotCorGraph: no visible global function definition for ‘new’
plotCorGraph: no visible global function definition for
  ‘igraph.from.graphNEL’
plotCorGraph: no visible global function definition for ‘V’
plotCorGraph: no visible global function definition for ‘V<-’
plotCorGraph: no visible global function definition for ‘E’
plotCorGraph: no visible global function definition for ‘E<-’
plotCorGraph: no visible global function definition for
  ‘layout.fruchterman.reingold’
plotCorGraph: no visible global function definition for ‘vcount’
plotCorGraph: no visible global function definition for
  ‘tkplot.fit.to.screen’
plotCorGraph: no visible global function definition for ‘plot’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘ggplot’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_density’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘aes’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_point’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_colour_gradientn’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘maPalette’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_x_discrete’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_hline’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘annotate’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_histogram’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_y_continuous’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_x_continuous’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_boxplot’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘theme_bw’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_jitter’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘position_jitter’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘theme’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘element_text’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘unit’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_linetype_manual’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_fill_manual’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘ggtitle’
plotDensAllAnnotInAllComp: no visible global function definition for
  ‘%dopar%’
plotDensAllAnnotInAllComp: no visible global function definition for
  ‘foreach’
plotDensOneAnnotInAllComp : vplayout: no visible global function
  definition for ‘viewport’
plotDensOneAnnotInAllComp: no visible global function definition for
  ‘ggsave’
plotMclust: no visible global function definition for ‘cdens’
plotMclust: no visible global function definition for ‘points’
plotMix: no visible global function definition for ‘shapiro.test’
plotMix: no visible global function definition for ‘cdens’
plotMix: no visible global function definition for ‘hist’
plotMix: no visible global function definition for ‘points’
plotMix : <anonymous>: no visible global function definition for
  ‘points’
plotMix: no visible global function definition for ‘lm’
plotMix: no visible global function definition for ‘axis’
plotNumVarComp: no visible global function definition for ‘ggplot’
plotNumVarComp: no visible global function definition for ‘geom_point’
plotNumVarComp: no visible global function definition for ‘aes’
plotNumVarComp: no visible global function definition for ‘geom_smooth’
plotNumVarComp: no visible binding for global variable ‘lm’
plotNumVarComp: no visible global function definition for
  ‘scale_colour_manual’
plotNumVarComp: no visible global function definition for
  ‘scale_shape_manual’
plotNumVarComp: no visible global function definition for ‘ggtitle’
plotNumVarComp: no visible global function definition for
  ‘scale_colour_gradientn’
plotNumVarComp: no visible global function definition for ‘maPalette’
plotPos2classInComp: no visible global function definition for ‘pdf’
plotPos2classInComp: no visible global function definition for ‘par’
plotPos2classInComp: no visible global function definition for ‘hist’
plotPos2classInComp: no visible global function definition for ‘plot’
plotPos2classInComp: no visible global function definition for ‘lm’
plotPos2classInComp: no visible global function definition for ‘axis’
plotPos2classInComp: no visible global function definition for ‘abline’
plotPos2classInComp: no visible global function definition for ‘legend’
plotPos2classInComp: no visible global function definition for
  ‘dev.off’
plotPosAnnotInComp : <anonymous>: no visible global function definition
  for ‘graphics.off’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘pdf’
plotPosOneAnnotInComp_ggplot : vplayout: no visible global function
  definition for ‘viewport’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘%dopar%’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘foreach’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘grid.newpage’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘pushViewport’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘viewport’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘grid.layout’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘dev.off’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘ggplot’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘geom_histogram’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘aes’
plotPosOneAnnotLevInComp_ggplot: no visible binding for global variable
  ‘..count..’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘scale_fill_manual’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘theme’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘element_text’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘unit’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘xlab’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘geom_point’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘scale_colour_gradientn’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘maPalette’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘geom_hline’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘annotate’
plotPosSamplesInComp: no visible global function definition for ‘pdf’
plotPosSamplesInComp: no visible global function definition for ‘par’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘chisq.test’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘par’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘hist’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘plot’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘lm’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘axis’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘legend’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘abline’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘points’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘quantile’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘maPalette’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘maColorBar’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘odd’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘mtext’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘title’
plotPosSamplesInComp: no visible global function definition for
  ‘dev.off’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘pdf’
plotPosSamplesInComp_ggplot : vplayout: no visible global function
  definition for ‘viewport’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘%dopar%’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘foreach’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘ggplot’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘geom_histogram’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘aes’
plotPosSamplesInComp_ggplot: no visible binding for global variable
  ‘..count..’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘theme’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘element_text’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘unit’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘xlab’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘ggtitle’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘geom_point’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘scale_colour_gradientn’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘maPalette’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘geom_hline’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘annotate’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘grid.newpage’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘pushViewport’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘viewport’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘grid.layout’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘dev.off’
plot_heatmapsOnSel: no visible global function definition for
  ‘maPalette’
plot_heatmapsOnSel: no visible global function definition for ‘%do%’
plot_heatmapsOnSel: no visible global function definition for ‘foreach’
plot_heatmapsOnSel: no visible global function definition for ‘pdf’
plot_heatmapsOnSel: no visible global function definition for
  ‘plot.new’
plot_heatmapsOnSel: no visible global function definition for ‘legend’
plot_heatmapsOnSel: no visible global function definition for ‘dev.off’
plot_heatmapsOnSel: no visible global function definition for ‘%dopar%’
plot_heatmapsOnSel: no visible global function definition for ‘plot’
plot_heatmapsOnSel: no visible global function definition for ‘par’
plot_heatmapsOnSel: no visible global function definition for
  ‘maColorBar’
plot_heatmapsOnSel: no visible global function definition for ‘odd’
qualVarAnalysis : <anonymous> : <anonymous>: no visible global function
  definition for ‘wilcox.test’
qualVarAnalysis : <anonymous> : <anonymous>: no visible global function
  definition for ‘kruskal.test’
qualVarAnalysis: no visible binding for global variable ‘p.adjust’
qualVarAnalysis: no visible global function definition for ‘%dopar%’
qualVarAnalysis: no visible global function definition for ‘foreach’
qualVarAnalysis : <anonymous>: no visible global function definition
  for ‘ggsave’
quantVarAnalysis : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor.test’
quantVarAnalysis: no visible binding for global variable ‘p.adjust’
quantVarAnalysis: no visible global function definition for ‘%dopar%’
quantVarAnalysis: no visible global function definition for ‘foreach’
quantVarAnalysis : <anonymous>: no visible global function definition
  for ‘ggsave’
readA: no visible global function definition for ‘read.table’
readS: no visible global function definition for ‘read.table’
runAn: no visible global function definition for ‘useMart’
runAn: no visible global function definition for ‘%do%’
runAn: no visible global function definition for ‘foreach’
runAn: no visible global function definition for ‘maPalette’
runCompareIcaSets: no visible global function definition for ‘%do%’
runCompareIcaSets: no visible global function definition for ‘foreach’
runEnrich: no visible global function definition for ‘llply’
runEnrich : <anonymous>: no visible global function definition for
  ‘na.omit’
runEnrich: no visible global function definition for ‘na.omit’
runEnrich: no visible global function definition for ‘listFilters’
runEnrich: no visible global function definition for ‘getBM’
runICA: no visible global function definition for ‘JADE’
runICA: no visible global function definition for ‘fastICA’
subIcaSet: no visible global function definition for ‘validObject’
wilcoxOrKruskalOnA: no visible global function definition for ‘%dopar%’
wilcoxOrKruskalOnA: no visible global function definition for ‘foreach’
wilcoxOrKruskalOnA: no visible global function definition for
  ‘wilcox.test’
wilcoxOrKruskalOnA: no visible global function definition for
  ‘kruskal.test’
writeGenes: no visible global function definition for ‘useMart’
writeGenes: no visible global function definition for ‘listFilters’
writeGenes: no visible global function definition for ‘listAttributes’
writeGenes: no visible global function definition for ‘getBM’
writeGenes: no visible global function definition for ‘xtable’
writeGenes: no visible global function definition for ‘capture.output’
writeGostatsHtmltable: no visible global function definition for
  ‘xtable’
writeGostatsHtmltable: no visible global function definition for
  ‘capture.output’
writeHtmlResTestsByAnnot: no visible global function definition for
  ‘llply’
writeHtmlResTestsByAnnot: no visible global function definition for
  ‘xtable’
writeHtmlResTestsByAnnot: no visible global function definition for
  ‘capture.output’
writeProjByComp: no visible global function definition for ‘useMart’
writeProjByComp: no visible global function definition for ‘%do%’
writeProjByComp: no visible global function definition for ‘foreach’
writeRnkFiles : <anonymous>: no visible global function definition for
  ‘write.table’
A<-,IcaSet: no visible global function definition for ‘validObject’
Afile<-,MineICAParams: no visible global function definition for
  ‘validObject’
S<-,IcaSet: no visible global function definition for ‘validObject’
SByGene<-,IcaSet: no visible global function definition for
  ‘validObject’
Sfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
[<-,IcaSet-ANY-ANY-ANY: no visible global function definition for
  ‘validObject’
[<-,MineICAParams-ANY-ANY-ANY: no visible global function definition
  for ‘validObject’
annot2col<-,MineICAParams: no visible global function definition for
  ‘validObject’
annotfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
chipManu<-,IcaSet: no visible global function definition for
  ‘validObject’
chipVersion<-,IcaSet: no visible global function definition for
  ‘validObject’
compNames<-,IcaSet: no visible global function definition for
  ‘validObject’
dat<-,IcaSet: no visible global function definition for ‘validObject’
datByGene<-,IcaSet: no visible global function definition for
  ‘validObject’
datfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
genesPath<-,ANY: no visible global function definition for
  ‘validObject’
indComp<-,IcaSet: no visible global function definition for
  ‘validObject’
initialize,IcaSet: no visible global function definition for ‘new’
initialize,IcaSet: no visible global function definition for ‘useMart’
initialize,IcaSet: no visible global function definition for
  ‘callNextMethod’
mart<-,IcaSet: no visible global function definition for ‘validObject’
organism<-,IcaSet: no visible global function definition for
  ‘validObject’
package<-,IcaSet: no visible global function definition for
  ‘validObject’
pvalCutoff<-,MineICAParams: no visible global function definition for
  ‘validObject’
refSamples<-,IcaSet: no visible global function definition for
  ‘validObject’
resPath<-,ANY: no visible global function definition for ‘validObject’
sampleNames<-,IcaSet: no visible global function definition for
  ‘callNextMethod’
selCutoff<-,MineICAParams: no visible global function definition for
  ‘validObject’
selectContrib,IcaSet-numeric-character: no visible global function
  definition for ‘%do%’
selectContrib,IcaSet-numeric-character: no visible global function
  definition for ‘foreach’
selectContrib,IcaSet-numeric-character: no visible binding for global
  variable ‘comp.proj’
selectContrib,IcaSet-numeric-character: no visible binding for global
  variable ‘cutt’
selectContrib,list-numeric-ANY: no visible global function definition
  for ‘%do%’
selectContrib,list-numeric-ANY: no visible global function definition
  for ‘foreach’
setA<-,IcaSet: no visible global function definition for ‘validObject’
setAfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
setAnnot2col<-,MineICAParams: no visible global function definition for
  ‘validObject’
setAnnotation<-,IcaSet: no visible global function definition for
  ‘validObject’
setAnnotfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
setChipManu<-,IcaSet: no visible global function definition for
  ‘validObject’
setChipVersion<-,IcaSet: no visible global function definition for
  ‘validObject’
setDatfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
setGenesPath<-,ANY: no visible global function definition for
  ‘validObject’
setIndComp<-,IcaSet: no visible global function definition for
  ‘validObject’
setLabelsComp<-,IcaSet: no visible global function definition for
  ‘validObject’
setMart<-,IcaSet: no visible global function definition for
  ‘validObject’
setPackage<-,IcaSet: no visible global function definition for
  ‘validObject’
setPvalCutoff<-,MineICAParams: no visible global function definition
  for ‘validObject’
setRefSamples<-,IcaSet: no visible global function definition for
  ‘validObject’
setResPath<-,ANY: no visible global function definition for
  ‘validObject’
setSByGene<-,IcaSet: no visible global function definition for
  ‘validObject’
setSelCutoff<-,MineICAParams: no visible global function definition for
  ‘validObject’
setSfile<-,MineICAParams: no visible global function definition for
  ‘validObject’
setTypeID<-,IcaSet: no visible global function definition for
  ‘validObject’
setWitGenes<-,IcaSet: no visible global function definition for
  ‘validObject’
show,IcaSet: no visible global function definition for ‘callNextMethod’
typeID<-,IcaSet: no visible global function definition for
  ‘validObject’
witGenes<-,IcaSet: no visible global function definition for
  ‘validObject’
Undefined global functions or variables:
  %do% %dopar% ..count.. E E<- JADE Mclust V V<- abline aes aggregate
  agnes annotate as.dendrogram as.dist as.hclust axis brewer.pal
  callNextMethod capture.output cdens chisq.test cluster cm.colors
  combn comp.proj conditional cor cor.test cutree cutt dev.off dist
  element_text fastICA foreach frame geneIdUniverse geneIdsByCategory
  geom_bar geom_boxplot geom_density geom_histogram geom_hline
  geom_jitter geom_point geom_smooth getBM getEG getSYMBOL ggplot
  ggsave ggtitle graphics.off grid.layout grid.newpage hclust
  heat.colors heat_hcl hist hyperGTest igraph.from.graphNEL kmeans
  kruskal.test layout layout.fruchterman.reingold legend listAttributes
  listFilters llply lm maColorBar maPalette median mtext na.omit new
  odd order.dendrogram p.adjust pam par pdf plot plot.new points
  position_jitter pushViewport quantile rainbow_hcl rcorr read.table
  reorder scale_colour_gradientn scale_colour_manual scale_fill_manual
  scale_linetype_manual scale_shape_manual scale_x_continuous
  scale_x_discrete scale_y_continuous shapiro.test sigCategories
  terrain_hcl theme theme_bw title tkplot.fit.to.screen unit useMart
  validObject vcount viewport wilcox.test write.table xlab xtable
Consider adding
  importFrom("grDevices", "cm.colors", "dev.off", "graphics.off",
             "heat.colors", "pdf")
  importFrom("graphics", "abline", "axis", "frame", "hist", "layout",
             "legend", "mtext", "par", "plot", "plot.new", "points",
             "title")
  importFrom("methods", "callNextMethod", "new", "validObject")
  importFrom("stats", "aggregate", "as.dendrogram", "as.dist",
             "as.hclust", "chisq.test", "cor", "cor.test", "cutree",
             "dist", "hclust", "kmeans", "kruskal.test", "lm", "median",
             "na.omit", "order.dendrogram", "p.adjust", "quantile",
             "reorder", "shapiro.test", "wilcox.test")
  importFrom("utils", "capture.output", "combn", "read.table",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/MineICA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MineICA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MineICA’ ...
** R
** data
** byte-compile and prepare 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	0.383	0.012	0.396
annotFeaturesComp	3.284	0.024	3.345
annotFeaturesWithBiomaRt	0.004	0.000	0.004
annotInGene	1.423	0.012	1.443
annotReciprocal	0.012	0.000	0.012
buildIcaSet	0.530	0.047	0.581
buildMineICAParams	0.037	0.030	0.069
class-IcaSet	0.249	0.016	1.567
class-MineICAParams	0.007	0.001	0.007
clusVarAnalysis	0.130	0.028	0.159
clusterFastICARuns	0.126	0.008	0.134
clusterSamplesByComp	1.043	0.023	1.072
clusterSamplesByComp_multiple	0.292	0.025	0.322
compareAn	0.826	0.029	0.859
compareAn2graphfile	0.624	0.018	0.650
compareGenes	0.001	0.001	0.002
cor2An	0.018	0.005	0.023
getProj	0.029	0.009	0.038
getSdExpr	0.003	0.000	0.004
hypergeoAn	0.002	0.000	0.002
nbOccByGeneInComp	0.019	0.002	0.021
nbOccInComp	0.155	0.030	0.186
nbOccInComp_simple	0.068	0.026	0.097
nodeAttrs	0.008	0.001	0.008
plotAllMix	0.679	0.005	0.697
plotCorGraph	1.063	0.038	1.112
plotDensAllAnnotInAllComp	0.002	0.001	0.001
plotDensOneAnnotInAllComp	0.002	0.000	0.002
plotMclust	0.087	0.001	0.089
plotMix	0.080	0.001	0.081
plotPosAnnotInComp	0.002	0.000	0.002
plotPosSamplesInComp	0.002	0.000	0.002
plot_heatmapsOnSel	0.003	0.000	0.003
qualVarAnalysis	0.191	0.037	0.230
quantVarAnalysis	0.189	0.037	0.229
relativePath	0.003	0.000	0.003
runAn	0.003	0.001	0.002
runCompareIcaSets	0.694	0.019	0.725
runEnrich	0.002	0.001	0.002
runICA	0.091	0.002	0.093
selectContrib	0.003	0.000	0.003
selectFeatures_IQR	0.149	0.017	0.165
selectWitnessGenes	0.244	0.021	0.268
writeGenes	0.005	0.001	0.006
writeGostatsHtmltable	0.011	0.001	0.012
writeProjByComp	0.002	0.000	0.002