Multiple platform build/check report for BioC 3.22 - CHECK results for MineICA on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4866
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4653
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4610
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 nebbiolo2

To the developers/maintainers of the MineICA package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: MineICA

Version: 1.49.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MineICA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MineICA_1.49.0.tar.gz

StartedAt: 2025-10-15 01:48:20 -0400 (Wed, 15 Oct 2025)

EndedAt: 2025-10-15 01:53:32 -0400 (Wed, 15 Oct 2025)

EllapsedTime: 312.3 seconds

RetCode: 1

Status: ERROR

CheckDir: MineICA.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MineICA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MineICA_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MineICA.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MineICA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MineICA’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 code 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 ... 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 ... NOTE
checkRd: (-1) clusterFastICARuns.Rd:47: Lost braces
    47 |   \item{...}{Additional parameters for code{funClus}}
       |                                            ^
checkRd: (-1) clusterFastICARuns.Rd:52: Lost braces
    52 |   item{W}{the estimated unmixing matrix}, \item{Iq}{Iq
       |       ^
checkRd: (-1) clusterFastICARuns.Rd:52: Lost braces
    52 |   item{W}{the estimated unmixing matrix}, \item{Iq}{Iq
       |          ^
checkRd: (-1) plotDensOneAnnotInAllComp.Rd:104: Lost braces
   104 |   code{\link{writeHtmlResTestsByAnnot}},
       |       ^
checkRd: (-1) plotDensOneAnnotInAllComp.Rd:105: Lost braces
   105 |   code{\link{wilcox.test}}, code{\link{kruskal.test}}
       |       ^
checkRd: (-1) plotDensOneAnnotInAllComp.Rd:105: Lost braces
   105 |   code{\link{wilcox.test}}, code{\link{kruskal.test}}
       |                                 ^
checkRd: (-1) runICA.Rd:44: Lost braces
    44 |   item{W}{the estimated unmixing matrix}}
       |       ^
checkRd: (-1) runICA.Rd:44: Lost braces
    44 |   item{W}{the estimated unmixing matrix}}
       |          ^
checkRd: (-1) writeProjByComp.Rd:38: Lost braces
    38 | their annotations, please remember to modify code{genesPath(params)}, or
       |                                                  ^
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'Alist.Rd':
  ‘class-IcaSet’

Missing link(s) in Rd file 'Slist.Rd':
  ‘class-IcaSet’

Missing link(s) in Rd file 'class-IcaSet.Rd':
  ‘class-IcaSet’

Missing link(s) in Rd file 'getComp.Rd':
  ‘class-IcaSet’

Missing link(s) in Rd file 'runAn.Rd':
  ‘[Category:class-GOHyperGParams]{GOHyperGParams}’

Non-topic package-anchored link(s) in Rd file 'buildMineICAParams.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'build_sortHeatmap.Rd':
  ‘[MineICA:class-IcaSet]{icaSet}’

Non-topic package-anchored link(s) in Rd file 'clusVarAnalysis.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'plotDensAllAnnotInAllComp.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'plotDensOneAnnotInAllComp.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'plotPosAnnotInComp.Rd':
  ‘[MineICA:class-IcaSet]{icaSet}’

Non-topic package-anchored link(s) in Rd file 'plotPosSamplesInComp.Rd':
  ‘[MineICA:class-IcaSet]{icaSet}’ ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'qualVarAnalysis.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'quantVarAnalysis.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'runAn.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'runEnrich.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

Non-topic package-anchored link(s) in Rd file 'writeHtmlResTestsByAnnot.Rd':
  ‘[MineICA:class-IcaSet]{IcaSet}’

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

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Alist.Rd: class-IcaSet
  Slist.Rd: class-IcaSet
  class-IcaSet.Rd: eSet, AssayData-class, makeDataPackage, eSet-class,
    class-IcaSet
  getComp.Rd: class-IcaSet
  hypergeoAn.Rd: GOstats
  plotDens2classInComp_plotOnly.Rd: ggplot2
  plotPosOneAnnotInComp_ggplot.Rd: geom_histogram
  plotPosOneAnnotLevInComp_ggplot.Rd: ggplot2
  runAn.Rd: GOstats
  runEnrich.Rd: GOstats
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MineICA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCorGraph
> ### Title: Plots graph using
> ### Aliases: plotCorGraph
> 
> ### ** Examples
> 
> dat1 <- data.frame(matrix(rnorm(10000),ncol=10,nrow=1000))
> rownames(dat1) <- paste("g", 1:1000, sep="")
> colnames(dat1) <- paste("s", 1:10, sep="")
> dat2 <- data.frame(matrix(rnorm(10000),ncol=10,nrow=1000))
> rownames(dat2) <- paste("g", 1:1000, sep="")
> colnames(dat2) <- paste("s", 1:10, sep="")
> 
> ## run ICA
> resJade1 <- runICA(X=dat1, nbComp=3, method = "JADE")
> resJade2 <- runICA(X=dat2, nbComp=3, method = "JADE")
> 
> ## build params
> params <- buildMineICAParams(resPath="toy/")
> 
> ## build IcaSet object
> icaSettoy1 <- buildIcaSet(params=params, A=data.frame(resJade1$A), S=data.frame(resJade1$S),
+                           dat=dat1, alreadyAnnot=TRUE)$icaSet
> icaSettoy2 <- buildIcaSet(params=params, A=data.frame(resJade2$A), S=data.frame(resJade2$S),
+                           dat=dat2, alreadyAnnot=TRUE)$icaSet
> icaSets <- list(icaSettoy1, icaSettoy2)
> 
> resCompareAn <- compareAn(icaSets=list(icaSettoy1,icaSettoy2), labAn=c("toy1","toy2"),
+                          type.corr="pearson", level="genes", cutoff_zval=0)
> 
> ## Build a graph where edges correspond to maximal correlation value (useVal="cor"),
> dataGraph <- compareAn2graphfile(listPairCor=resCompareAn, useMax=TRUE, useVal="cor", file="myGraph.txt")
> 
> ## construction of the data.frame with the node description
> nbComp <- rep(3,2) #each IcaSet contains 3 components
> nbAn <- 2 # we are comparing 2 IcaSets
> # labels of components created as comp*i*
> labComp <- foreach(icaSet=icaSets, nb=nbComp, an=1:nbAn) %do% {
+                   paste(rep("comp",sum(nb)),1:nbComp(icaSet),sep = "")}
> 
> # creation of the data.frame with the node description
> nodeDescr <- nodeAttrs(nbAn = nbAn, nbComp = nbComp, labComp = labComp,
+                        labAn = c("toy1","toy2"), file = "nodeInfo.txt")
> 
> ## Plot correlation graph, slightly move the attached nodes to make the cliques visible
> ## use tkplot=TRUE to have an interactive graph
> res <- plotCorGraph(title = "Compare toy 1 and 2", dataGraph = dataGraph, nodeName = "indComp", tkplot = FALSE,
+                  nodeAttrs = nodeDescr, edgeWeight = "cor", nodeShape = "labAn", reciproCol = "reciprocal")
Warning in brewer.pal(nbAn, "Set3") :
  minimal value for n is 3, returning requested palette with 3 different levels

Error:
! The `area` argument of `layout_with_fr()` was deprecated in igraph
  0.8.0 and is now defunct.
Backtrace:
    ▆
 1. └─MineICA::plotCorGraph(...)
 2.   └─igraph::layout.fruchterman.reingold(...)
 3.     ├─igraph:::do_call(layout_with_fr, .args = c(list(...), params))
 4.     │ └─base::eval(call, .env)
 5.     │   └─base::eval(call, .env)
 6.     └─igraph::layout_with_fr(...)
 7.       └─lifecycle::deprecate_stop("0.8.0", "layout_with_fr(area = )")
 8.         └─lifecycle:::deprecate_stop0(msg)
 9.           └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
clusterFastICARuns 2.952  0.337  20.105
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MineICA.Rcheck/00check.log’
for details.

Installation output

MineICA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MineICA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MineICA’ ...
** this is package ‘MineICA’ version ‘1.49.0’
** 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

name	user	system	elapsed
annotFeatures	0.307	0.014	0.320
annotFeaturesComp	2.678	0.021	2.699
annotFeaturesWithBiomaRt	0.000	0.000	0.001
annotInGene	1.245	0.059	1.304
annotReciprocal	0.003	0.001	0.004
buildIcaSet	0.246	0.014	0.260
buildMineICAParams	0.007	0.004	0.011
class-IcaSet	0.208	0.021	0.797
class-MineICAParams	0.001	0.001	0.002
clusVarAnalysis	0.067	0.019	0.085
clusterFastICARuns	2.952	0.337	20.105
clusterSamplesByComp	0.647	0.008	0.657
clusterSamplesByComp_multiple	0.141	0.009	0.150
compareAn	0.397	0.051	0.449
compareAn2graphfile	0.341	0.026	0.368
compareGenes	0	0	0
cor2An	0.016	0.000	0.015
getProj	0.024	0.001	0.025
getSdExpr	0.002	0.000	0.001
hypergeoAn	0	0	0
nbOccByGeneInComp	0.009	0.000	0.009
nbOccInComp	0.087	0.006	0.092
nbOccInComp_simple	0.033	0.005	0.038
nodeAttrs	0.003	0.000	0.004
plotAllMix	0.418	0.010	0.428