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BioC 3.4: CHECK report for MineICA on morelia

This page was generated on 2016-09-21 03:52:11 -0700 (Wed, 21 Sep 2016).

Package 748/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MineICA 1.13.0
Anne Biton
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MineICA
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MineICA_1.13.0.tar.gz
StartedAt: 2016-09-20 09:20:27 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:23:15 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 168.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MineICA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MineICA_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/MineICA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.13.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 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.
* 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 : <anonymous>: no visible global function definition for
  ‘sd’
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 ‘sd’
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’
getSdExpr : <anonymous>: no visible global function definition for ‘sd’
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 binding for global variable ‘sd’
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 binding for global variable ‘var’
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 global function
  definition for ‘sd’
selectContrib,IcaSet-numeric-character: no visible binding for global
  variable ‘cutt’
selectContrib,list-numeric-ANY: no visible global function definition
  for ‘sd’
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 sd shapiro.test sigCategories
  terrain_hcl theme theme_bw title tkplot.fit.to.screen unit useMart
  validObject var 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", "sd", "shapiro.test", "var", "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 ... WARNING
Missing link or links in documentation object 'plotDens2classInComp_plotOnly.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotPosOneAnnotLevInComp_ggplot.Rd':
  ‘ggplot2’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/MineICA.Rcheck/00check.log’
for details.


MineICA.Rcheck/00install.out:

* 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)

MineICA.Rcheck/MineICA-Ex.timings:

nameusersystemelapsed
annotFeatures0.1970.0100.206
annotFeaturesComp1.6550.0141.670
annotFeaturesWithBiomaRt0.0010.0000.002
annotInGene0.7690.0110.780
annotReciprocal0.0060.0000.006
buildIcaSet0.3930.0200.438
buildMineICAParams0.0190.0140.036
class-IcaSet0.1460.0211.113
class-MineICAParams0.0040.0000.005
clusVarAnalysis0.1250.0160.142
clusterFastICARuns0.0890.0040.094
clusterSamplesByComp0.8860.0190.903
clusterSamplesByComp_multiple0.2550.0140.270
compareAn0.5730.0140.588
compareAn2graphfile0.4250.0130.440
compareGenes000
cor2An0.0150.0040.018
getProj0.0240.0080.033
getSdExpr0.0020.0000.002
hypergeoAn0.0000.0000.001
nbOccByGeneInComp0.0130.0010.014
nbOccInComp0.1130.0150.129
nbOccInComp_simple0.0490.0150.063
nodeAttrs0.0050.0010.006
plotAllMix0.5740.0041.195
plotCorGraph0.9650.0200.988
plotDensAllAnnotInAllComp0.0010.0010.001
plotDensOneAnnotInAllComp0.0010.0000.001
plotMclust0.0680.0010.069
plotMix0.0640.0000.065
plotPosAnnotInComp0.0000.0000.001
plotPosSamplesInComp0.0010.0000.001
plot_heatmapsOnSel0.0010.0000.002
qualVarAnalysis0.0810.0140.096
quantVarAnalysis0.1250.0200.145
relativePath0.0010.0000.001
runAn0.0010.0000.001
runCompareIcaSets0.8640.0150.881
runEnrich000
runICA0.0760.0010.077
selectContrib0.0020.0000.002
selectFeatures_IQR0.1200.0140.134
selectWitnessGenes0.1840.0180.202
writeGenes0.0020.0000.002
writeGostatsHtmltable0.0090.0010.009
writeProjByComp0.0000.0000.001