############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MineICA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MineICA_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MineICA.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MineICA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MineICA’ version ‘1.47.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 : : : no visible global function definition for ‘median’ annotFeaturesComp : : 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 : : : no visible global function definition for ‘chisq.test’ clusVarAnalysis : : : : 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 : : 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 : : 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 : : 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 : : no visible global function definition for ‘%dopar%’ mergeGostatsResults : : no visible global function definition for ‘foreach’ mergeGostatsResults : : no visible global function definition for ‘xtable’ mergeGostatsResults : : no visible global function definition for ‘capture.output’ mergeGostatsResults : : 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 : : 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 : : 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 : : no visible global function definition for ‘chisq.test’ plotPosSamplesInComp : : no visible global function definition for ‘par’ plotPosSamplesInComp : : no visible global function definition for ‘hist’ plotPosSamplesInComp : : no visible global function definition for ‘lm’ plotPosSamplesInComp : : no visible global function definition for ‘axis’ plotPosSamplesInComp : : no visible global function definition for ‘legend’ plotPosSamplesInComp : : no visible global function definition for ‘abline’ plotPosSamplesInComp : : no visible global function definition for ‘points’ plotPosSamplesInComp : : no visible global function definition for ‘quantile’ plotPosSamplesInComp : : no visible global function definition for ‘maPalette’ plotPosSamplesInComp : : no visible global function definition for ‘maColorBar’ plotPosSamplesInComp : : no visible global function definition for ‘odd’ plotPosSamplesInComp : : no visible global function definition for ‘mtext’ plotPosSamplesInComp : : 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 : : : no visible global function definition for ‘wilcox.test’ qualVarAnalysis : : : 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 : : no visible global function definition for ‘ggsave’ quantVarAnalysis : : : 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 : : 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 : : 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 : : 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 or links in Rd file 'Alist.Rd': ‘class-IcaSet’ Missing link or links in Rd file 'Slist.Rd': ‘class-IcaSet’ Missing link or links in Rd file 'class-IcaSet.Rd': ‘class-IcaSet’ Missing link or links in Rd file 'getComp.Rd': ‘class-IcaSet’ Missing link or links in Rd file 'runAn.Rd': ‘[Category:class-GOHyperGParams]{GOHyperGParams}’ 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clusterFastICARuns 1.323 0.242 29.9 * 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: 3 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/MineICA.Rcheck/00check.log’ for details.