############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathVar_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/pathVar.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pathVar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathVar’ version ‘1.26.0’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘pathVar’ 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 diagnosticsVarPlots: no visible binding for global variable ‘avg’ diagnosticsVarPlots: no visible binding for global variable ‘standDev’ diagnosticsVarPlots: no visible binding for global variable ‘medAbsDev’ diagnosticsVarPlots: no visible binding for global variable ‘cv’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘avg’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘standDev’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘medAbsDev’ diagnosticsVarPlotsTwoSample: no visible binding for global variable ‘cv’ pathVarOneSample: no visible binding for global variable ‘APval’ pathVarOneSample: no visible binding for global variable ‘PercOfGenesInPway’ pathVarTwoSamplesCont: no visible binding for global variable ‘APval’ pathVarTwoSamplesCont: no visible binding for global variable ‘PercOfGenesInPway’ pathVarTwoSamplesDisc: no visible binding for global variable ‘APval’ pathVarTwoSamplesDisc: no visible binding for global variable ‘PercOfGenesInPway’ plotAllTwoSampleDistributionCounts: no visible binding for global variable ‘Cluster’ plotAllTwoSampleDistributionCounts: no visible binding for global variable ‘Number_of_genes’ plotOneSample: no visible binding for global variable ‘Cluster’ plotOneSample: no visible binding for global variable ‘Number_of_genes’ plotTwoSamplesCont: no visible binding for global variable ‘PwayName’ plotTwoSamplesCont: no visible binding for global variable ‘NumOfGenesFromDataSetInPathway’ plotTwoSamplesCont: no visible binding for global variable ‘value’ plotTwoSamplesCont: no visible binding for global variable ‘..density..’ plotTwoSamplesCont: no visible binding for global variable ‘group’ plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’ plotTwoSamplesDisc: no visible binding for global variable ‘Number_of_genes’ sigOneSample: no visible binding for global variable ‘APval’ sigOneSample: no visible binding for global variable ‘PwayName’ sigTwoSamplesCont: no visible binding for global variable ‘APval’ sigTwoSamplesCont: no visible binding for global variable ‘PwayName’ sigTwoSamplesDisc: no visible binding for global variable ‘APval’ sigTwoSamplesDisc: no visible binding for global variable ‘PwayName’ Undefined global functions or variables: ..density.. APval Cluster NumOfGenesFromDataSetInPathway Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev standDev value * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sigPway 119.643 1.364 121.645 diagnosticsVarPlots 54.907 0.827 56.048 diagnosticsVarPlotsTwoSample 32.751 0.405 33.233 plotAllTwoSampleDistributionCounts 5.998 0.769 6.779 plotPway 6.454 0.068 6.548 saveAsPDF 5.779 0.037 5.823 getGenes 5.024 0.114 5.148 pathVarTwoSamplesCont 5.002 0.051 5.070 * 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 NOTE See ‘/Users/biocbuild/bbs-3.15-bioc/meat/pathVar.Rcheck/00check.log’ for details.