############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:interactiveDisplay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings interactiveDisplay_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/interactiveDisplay.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘interactiveDisplay/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘interactiveDisplay’ version ‘1.44.0’ * 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' NOTE Package which this enhances but not available for checking: ‘rstudio’ * 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 ‘interactiveDisplay’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .altgr : : no visible global function definition for ‘elementMetadata’ .altgr : : no visible global function definition for ‘seqlevels<-’ .bicgo : : no visible binding for global variable ‘GO.db’ .bicgo : : no visible global function definition for ‘exprs’ .bicgo : : no visible global function definition for ‘cutree’ .bicgo : : no visible global function definition for ‘hclust’ .bicgo : : no visible global function definition for ‘dist’ .bicgo : : no visible global function definition for ‘cim’ .choose_gen: no visible global function definition for ‘ucscGenomes’ .simplenet : : no visible global function definition for ‘cutree’ .simplenet : : no visible global function definition for ‘rainbow’ .simplenet : : hc: no visible global function definition for ‘hclust’ .simplenet : : hc: no visible global function definition for ‘dist’ .simplenet : : dm: no visible global function definition for ‘dist’ .usePackage: no visible global function definition for ‘installed.packages’ ggheat: no visible global function definition for ‘colorRampPalette’ ggheat: no visible binding for global variable ‘Var2’ ggheat: no visible binding for global variable ‘Var1’ ggheat: no visible binding for global variable ‘value’ ggheat: no visible global function definition for ‘coord_flip’ grid2jssvg: no visible global function definition for ‘png’ grid2jssvg: no visible global function definition for ‘dev.off’ subgr: no visible global function definition for ‘seqnames’ subgr: no visible global function definition for ‘seqlevels<-’ subgr: no visible global function definition for ‘ranges’ subgr2: no visible global function definition for ‘seqnames’ subgr2: no visible global function definition for ‘seqlevels<-’ subgr2: no visible global function definition for ‘ranges’ display,ExpressionSet : : no visible global function definition for ‘exprs’ display,ExpressionSet : : no visible global function definition for ‘experimentData’ display,ExpressionSet : : no visible binding for global variable ‘GO.db’ display,ExpressionSet : : no visible global function definition for ‘cutree’ display,ExpressionSet : : no visible global function definition for ‘rainbow’ display,ExpressionSet : : hc: no visible global function definition for ‘hclust’ display,ExpressionSet : : hc: no visible global function definition for ‘dist’ display,ExpressionSet : : dm: no visible global function definition for ‘dist’ display,ExpressionSet : : no visible global function definition for ‘as.dendrogram’ display,ExpressionSet : : : : no visible global function definition for ‘is.leaf’ display,ExpressionSet : : no visible global function definition for ‘dendrapply’ display,GRanges: no visible global function definition for ‘mcols’ display,GRanges : : no visible global function definition for ‘AnnotationTrack’ display,GRanges : : no visible global function definition for ‘GenomeAxisTrack’ display,GRanges : : no visible global function definition for ‘IdeogramTrack’ display,GRanges : : no visible global function definition for ‘plotTracks’ display,GRanges : : no visible global function definition for ‘layout_circle’ display,GRanges : : no visible binding for global variable ‘seqnames’ display,GRanges : : no visible global function definition for ‘seqnames’ display,GRanges : : no visible global function definition for ‘ranges’ display,GRanges : : no visible global function definition for ‘ucscGenomes’ display,GRanges : : no visible global function definition for ‘GRanges’ display,GRanges : : no visible global function definition for ‘IRanges’ display,GRanges : : no visible global function definition for ‘seqlengths<-’ display,GRanges : : no visible global function definition for ‘seqlengths’ display,GRangesList : : no visible global function definition for ‘mcols’ display,GRangesList : : no visible global function definition for ‘AnnotationTrack’ display,GRangesList : : no visible global function definition for ‘GenomeAxisTrack’ display,GRangesList : : no visible global function definition for ‘IdeogramTrack’ display,GRangesList : : no visible global function definition for ‘plotTracks’ display,GRangesList : : no visible global function definition for ‘layout_circle’ display,GRangesList : : no visible binding for global variable ‘seqnames’ display,GRangesList : : no visible global function definition for ‘seqnames’ display,GRangesList : : no visible global function definition for ‘ranges’ display,GRangesList : : no visible global function definition for ‘ucscGenomes’ display,GRangesList : : no visible global function definition for ‘GRanges’ display,GRangesList : : no visible global function definition for ‘IRanges’ display,GRangesList : : no visible global function definition for ‘seqlengths<-’ display,GRangesList : : no visible global function definition for ‘seqlengths’ display,GRangesList : : no visible global function definition for ‘GRangesList’ display,MRexperiment : : no visible global function definition for ‘MRcounts’ display,MRexperiment : : no visible global function definition for ‘pData’ display,MRexperiment : : no visible global function definition for ‘colorRampPalette’ display,MRexperiment : : no visible global function definition for ‘legend’ display,MRexperiment : : no visible global function definition for ‘plotFeature’ display,MRexperiment : : no visible global function definition for ‘plotOrd’ display,MRexperiment : : no visible global function definition for ‘libSize’ display,MRexperiment : : no visible global function definition for ‘fData’ display,RangedSummarizedExperiment : : no visible global function definition for ‘seqnames’ display,RangedSummarizedExperiment : : no visible global function definition for ‘rowRanges’ display,RangedSummarizedExperiment : : no visible global function definition for ‘assays’ display,RangedSummarizedExperiment : : no visible global function definition for ‘colorRampPalette’ display,RangedSummarizedExperiment : : no visible binding for global variable ‘Var1’ display,RangedSummarizedExperiment : : no visible binding for global variable ‘Var2’ display,RangedSummarizedExperiment : : no visible binding for global variable ‘value’ Undefined global functions or variables: AnnotationTrack GO.db GRanges GRangesList GenomeAxisTrack IRanges IdeogramTrack MRcounts Var1 Var2 as.dendrogram assays cim colorRampPalette coord_flip cutree dendrapply dev.off dist elementMetadata experimentData exprs fData hclust installed.packages is.leaf layout_circle legend libSize mcols pData plotFeature plotOrd plotTracks png rainbow ranges rowRanges seqlengths seqlengths<- seqlevels<- seqnames ucscGenomes value Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "png", "rainbow") importFrom("graphics", "legend") importFrom("stats", "as.dendrogram", "cutree", "dendrapply", "dist", "hclust", "is.leaf") importFrom("utils", "installed.packages") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/interactiveDisplay.Rcheck/00check.log’ for details.