Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-02-01 11:07:17 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MineICA on palomino4


To the developers/maintainers of the MineICA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MineICA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1206/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MineICA 1.38.0  (landing page)
Anne Biton
Snapshot Date: 2023-01-31 14:00:04 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/MineICA
git_branch: RELEASE_3_16
git_last_commit: 4d1fbc6
git_last_commit_date: 2022-11-01 11:07:52 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MineICA
Version: 1.38.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MineICA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MineICA_1.38.0.tar.gz
StartedAt: 2023-02-01 03:26:21 -0500 (Wed, 01 Feb 2023)
EndedAt: 2023-02-01 03:31:06 -0500 (Wed, 01 Feb 2023)
EllapsedTime: 284.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MineICA.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MineICA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MineICA_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MineICA.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.38.0'
* 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 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 1.27   0.13   33.97
class-IcaSet       0.19   0.03    7.06
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/MineICA.Rcheck/00check.log'
for details.



Installation output

MineICA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MineICA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'MineICA' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MineICA)

Tests output


Example timings

MineICA.Rcheck/MineICA-Ex.timings

nameusersystemelapsed
annotFeatures0.410.010.44
annotFeaturesComp2.550.022.68
annotFeaturesWithBiomaRt000
annotInGene1.280.001.28
annotReciprocal000
buildIcaSet0.290.020.69
buildMineICAParams0.000.000.77
class-IcaSet0.190.037.06
class-MineICAParams000
clusVarAnalysis0.080.010.53
clusterFastICARuns 1.27 0.1333.97
clusterSamplesByComp1.560.001.98
clusterSamplesByComp_multiple0.140.010.55
compareAn0.610.021.01
compareAn2graphfile0.470.010.90
compareGenes000
cor2An0.010.020.03
getProj0.050.000.04
getSdExpr000
hypergeoAn000
nbOccByGeneInComp0.030.000.03
nbOccInComp0.130.030.58
nbOccInComp_simple0.030.020.42
nodeAttrs000
plotAllMix0.840.010.86
plotCorGraph0.590.031.02
plotDensAllAnnotInAllComp000
plotDensOneAnnotInAllComp000
plotMclust0.130.000.12
plotMix0.120.000.13
plotPosAnnotInComp000
plotPosSamplesInComp000
plot_heatmapsOnSel000
qualVarAnalysis0.070.020.55
quantVarAnalysis0.110.030.73
relativePath000
runAn000
runCompareIcaSets0.320.000.70
runEnrich000
runICA0.050.000.05
selectContrib000
selectFeatures_IQR0.080.010.09
selectWitnessGenes0.090.000.48
writeGenes000
writeGostatsHtmltable0.010.000.02
writeProjByComp000