############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tRanslatome_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/tRanslatome.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tRanslatome/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tRanslatome’ version ‘1.36.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'limma', 'sigPathway', 'anota', 'DESeq2', 'edgeR', 'RankProd', 'topGO', 'org.Hs.eg.db', 'GOSemSim', 'Heatplus', 'gplots', 'plotrix', 'Biobase' 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 ‘tRanslatome’ 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE computeGeneListEnrichment: no visible global function definition for ‘data’ computeGeneListEnrichment: no visible binding for global variable ‘tRanslatomeSampleData’ computeGeneListEnrichment: no visible global function definition for ‘fisher.test’ computeGeneListEnrichment: no visible global function definition for ‘p.adjust’ createspecifictable: no visible global function definition for ‘str’ createspecifictable: no visible global function definition for ‘p.adjust’ methodANOTA: no visible global function definition for ‘p.adjust’ methodEdgeR: no visible global function definition for ‘p.adjust’ methodLimma: no visible global function definition for ‘model.matrix’ methodLimma: no visible global function definition for ‘lmFit’ methodLimma: no visible global function definition for ‘p.adjust’ methodTTest: no visible global function definition for ‘p.adjust’ CVplot,DEGs: no visible global function definition for ‘pdf’ CVplot,DEGs: no visible global function definition for ‘postscript’ CVplot,DEGs: no visible global function definition for ‘jpeg’ CVplot,DEGs: no visible global function definition for ‘par’ CVplot,DEGs: no visible global function definition for ‘layout’ CVplot,DEGs: no visible global function definition for ‘points’ CVplot,DEGs: no visible global function definition for ‘abline’ CVplot,DEGs: no visible global function definition for ‘legend’ CVplot,DEGs: no visible global function definition for ‘text’ CVplot,DEGs: no visible global function definition for ‘dev.off’ GOEnrichment,DEGs: no visible global function definition for ‘toTable’ Heatmap,EnrichedSets: no visible global function definition for ‘pdf’ Heatmap,EnrichedSets: no visible global function definition for ‘postscript’ Heatmap,EnrichedSets: no visible global function definition for ‘jpeg’ Heatmap,EnrichedSets: no visible global function definition for ‘png’ Heatmap,EnrichedSets: no visible global function definition for ‘dev.off’ Heatmap,GOsets: no visible global function definition for ‘pdf’ Heatmap,GOsets: no visible global function definition for ‘postscript’ Heatmap,GOsets: no visible global function definition for ‘jpeg’ Heatmap,GOsets: no visible global function definition for ‘png’ Heatmap,GOsets: no visible global function definition for ‘dev.off’ Histogram,DEGs: no visible global function definition for ‘pdf’ Histogram,DEGs: no visible global function definition for ‘postscript’ Histogram,DEGs: no visible global function definition for ‘jpeg’ Histogram,DEGs: no visible global function definition for ‘par’ Histogram,DEGs: no visible global function definition for ‘barplot’ Histogram,DEGs: no visible global function definition for ‘legend’ Histogram,DEGs: no visible global function definition for ‘mtext’ Histogram,DEGs: no visible global function definition for ‘dev.off’ IdentityPlot,GOsims: no visible global function definition for ‘pdf’ IdentityPlot,GOsims: no visible global function definition for ‘postscript’ IdentityPlot,GOsims: no visible global function definition for ‘jpeg’ IdentityPlot,GOsims: no visible global function definition for ‘barplot’ IdentityPlot,GOsims: no visible global function definition for ‘dev.off’ MAplot,DEGs: no visible global function definition for ‘pdf’ MAplot,DEGs: no visible global function definition for ‘postscript’ MAplot,DEGs: no visible global function definition for ‘jpeg’ MAplot,DEGs: no visible global function definition for ‘par’ MAplot,DEGs: no visible global function definition for ‘layout’ MAplot,DEGs: no visible global function definition for ‘points’ MAplot,DEGs: no visible global function definition for ‘abline’ MAplot,DEGs: no visible global function definition for ‘legend’ MAplot,DEGs: no visible global function definition for ‘text’ MAplot,DEGs: no visible global function definition for ‘dev.off’ Radar,EnrichedSets: no visible global function definition for ‘pdf’ Radar,EnrichedSets: no visible global function definition for ‘postscript’ Radar,EnrichedSets: no visible global function definition for ‘jpeg’ Radar,EnrichedSets: no visible global function definition for ‘png’ Radar,EnrichedSets: no visible global function definition for ‘par’ Radar,EnrichedSets: no visible global function definition for ‘legend’ Radar,EnrichedSets: no visible global function definition for ‘dev.off’ Radar,GOsets: no visible global function definition for ‘pdf’ Radar,GOsets: no visible global function definition for ‘postscript’ Radar,GOsets: no visible global function definition for ‘jpeg’ Radar,GOsets: no visible global function definition for ‘png’ Radar,GOsets: no visible global function definition for ‘par’ Radar,GOsets: no visible global function definition for ‘legend’ Radar,GOsets: no visible global function definition for ‘dev.off’ SDplot,DEGs: no visible global function definition for ‘pdf’ SDplot,DEGs: no visible global function definition for ‘postscript’ SDplot,DEGs: no visible global function definition for ‘jpeg’ SDplot,DEGs: no visible global function definition for ‘par’ SDplot,DEGs: no visible global function definition for ‘layout’ SDplot,DEGs: no visible global function definition for ‘points’ SDplot,DEGs: no visible global function definition for ‘abline’ SDplot,DEGs: no visible global function definition for ‘legend’ SDplot,DEGs: no visible global function definition for ‘text’ SDplot,DEGs: no visible global function definition for ‘dev.off’ Scatterplot,DEGs: no visible global function definition for ‘pdf’ Scatterplot,DEGs: no visible global function definition for ‘postscript’ Scatterplot,DEGs: no visible global function definition for ‘jpeg’ Scatterplot,DEGs: no visible global function definition for ‘mtext’ Scatterplot,DEGs: no visible global function definition for ‘cor.test’ Scatterplot,DEGs: no visible global function definition for ‘points’ Scatterplot,DEGs: no visible global function definition for ‘abline’ Scatterplot,DEGs: no visible global function definition for ‘legend’ Scatterplot,DEGs: no visible global function definition for ‘text’ Scatterplot,DEGs: no visible global function definition for ‘dev.off’ SimilarityPlot,GOsims: no visible global function definition for ‘pdf’ SimilarityPlot,GOsims: no visible global function definition for ‘postscript’ SimilarityPlot,GOsims: no visible global function definition for ‘jpeg’ SimilarityPlot,GOsims: no visible global function definition for ‘barplot’ SimilarityPlot,GOsims: no visible global function definition for ‘legend’ SimilarityPlot,GOsims: no visible global function definition for ‘dev.off’ computeDEGs,TranslatomeDataset : : no visible global function definition for ‘sd’ show,DEGs: no visible global function definition for ‘head’ show,GOsims: no visible global function definition for ‘head’ show,TranslatomeDataset: no visible global function definition for ‘head’ Undefined global functions or variables: abline barplot cor.test data dev.off fisher.test head jpeg layout legend lmFit model.matrix mtext p.adjust par pdf png points postscript sd str tRanslatomeSampleData text toTable Consider adding importFrom("grDevices", "dev.off", "jpeg", "pdf", "png", "postscript") importFrom("graphics", "abline", "barplot", "layout", "legend", "mtext", "par", "points", "text") importFrom("stats", "cor.test", "fisher.test", "model.matrix", "p.adjust", "sd") importFrom("utils", "data", "head", "str") 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 ... WARNING Found the following significant warnings: Warning: 'RGBColVec' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed GOComparison 14.241 0.941 15.223 GOEnrichment 11.225 0.185 11.428 * 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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/tRanslatome.Rcheck/00check.log’ for details.