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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MineICA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MineICA_1.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MineICA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MineICA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MineICA’ version ‘1.40.0’
* 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 dependencies in R code ... WARNING
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.
Missing or unexported object: ‘GOstats::geneIdsByCategory’
':::' 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
‘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 ‘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 ‘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’
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 ‘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 ‘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 ‘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 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.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.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 ... WARNING
Missing link or links in documentation object 'Alist.Rd':
‘class-IcaSet’
Missing link or links in documentation object 'Slist.Rd':
‘class-IcaSet’
Missing link or links in documentation object 'class-IcaSet.Rd':
‘class-IcaSet’
Missing link or links in documentation object 'getComp.Rd':
‘class-IcaSet’
Missing link or links in documentation object 'runAn.Rd':
‘[Category:class-GOHyperGParams]{GOHyperGParams}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
‘MineICAParams’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clusterFastICARuns 1.387 0.226 64.84
* 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: 3 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MineICA.Rcheck/00check.log’
for details.
