############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqGSEA_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SeqGSEA.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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SeqGSEA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SeqGSEA’ version ‘1.44.0’ * 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 ‘SeqGSEA’ 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 dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘estiExonProbVar’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DENBStat4GSEA: no visible global function definition for ‘colData’ DENBStatPermut4GSEA: no visible global function definition for ‘%dopar%’ DENBStatPermut4GSEA: no visible global function definition for ‘foreach’ DENBStatPermut4GSEA: no visible binding for global variable ‘i’ DENBTest: no visible global function definition for ‘colData’ DENBTest: no visible global function definition for ‘p.adjust’ DEpermutePval: no visible global function definition for ‘p.adjust’ DSpermute4GSEA: no visible global function definition for ‘%dopar%’ DSpermute4GSEA: no visible global function definition for ‘foreach’ DSpermute4GSEA : : no visible binding for global variable ‘i’ DSpermutePval: no visible global function definition for ‘p.adjust’ calES.perm: no visible global function definition for ‘%dopar%’ calES.perm: no visible global function definition for ‘foreach’ calES.perm: no visible binding for global variable ‘i’ calES.perm: no visible global function definition for ‘%do%’ calES.perm: no visible binding for global variable ‘j’ loadExonCountData : : no visible global function definition for ‘read.table’ nbinomTestForMatrices : : no visible global function definition for ‘dnbinom’ plotES : : no visible global function definition for ‘density’ plotES: no visible global function definition for ‘density’ plotES : : no visible global function definition for ‘points’ plotES: no visible global function definition for ‘points’ plotES: no visible global function definition for ‘colors’ plotES: no visible global function definition for ‘lines’ plotES: no visible global function definition for ‘legend’ plotES: no visible global function definition for ‘dev.off’ plotGeneScore: no visible global function definition for ‘lines’ plotGeneScore: no visible global function definition for ‘colors’ plotGeneScore: no visible global function definition for ‘points’ plotGeneScore: no visible global function definition for ‘matlines’ plotGeneScore: no visible global function definition for ‘legend’ plotGeneScore: no visible global function definition for ‘dev.off’ plotSig: no visible global function definition for ‘points’ plotSig: no visible global function definition for ‘colors’ plotSig: no visible global function definition for ‘legend’ plotSig: no visible global function definition for ‘dev.off’ plotSigGeneSet: no visible global function definition for ‘par’ plotSigGeneSet: no visible global function definition for ‘layout’ plotSigGeneSet: no visible global function definition for ‘lines’ plotSigGeneSet : : no visible global function definition for ‘lines’ plotSigGeneSet: no visible global function definition for ‘colors’ plotSigGeneSet: no visible global function definition for ‘text’ plotSigGeneSet: no visible global function definition for ‘density’ plotSigGeneSet: no visible global function definition for ‘legend’ plotSigGeneSet: no visible global function definition for ‘dev.off’ runDESeq: no visible global function definition for ‘DataFrame’ runSeqGSEA: no visible global function definition for ‘makeCluster’ runSeqGSEA: no visible global function definition for ‘write.table’ signifES : : no visible global function definition for ‘median’ writeScores: no visible global function definition for ‘write.table’ writeSigGeneSet: no visible global function definition for ‘write.table’ Undefined global functions or variables: %do% %dopar% DataFrame colData colors density dev.off dnbinom foreach i j layout legend lines makeCluster matlines median p.adjust par points read.table text write.table Consider adding importFrom("grDevices", "colors", "dev.off") importFrom("graphics", "layout", "legend", "lines", "matlines", "par", "points", "text") importFrom("stats", "density", "dnbinom", "median", "p.adjust") importFrom("utils", "read.table", "write.table") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed topDEGenes 24.783 0.280 29.415 DENBStatPermut4GSEA 23.722 0.233 28.306 DEpermutePval 23.554 0.283 29.028 DSpermutePval 13.783 0.164 17.100 normFactor 13.658 0.131 16.948 topDSGenes 13.641 0.122 16.278 topDSExons 13.005 0.174 15.396 DSresultGeneTable 13.007 0.108 15.991 scoreNormalization 12.872 0.098 15.368 DSresultExonTable 12.850 0.109 15.632 DSpermute4GSEA 12.429 0.236 15.465 genpermuteMat 11.861 0.199 14.586 DENBStat4GSEA 4.790 0.396 6.550 plotES 4.398 0.061 5.538 plotSig 4.249 0.087 5.403 plotSigGeneSet 4.251 0.038 5.262 GSEnrichAnalyze 4.211 0.034 5.192 GSEAresultTable 4.196 0.046 5.294 calES.perm 4.200 0.031 5.212 topGeneSets 4.150 0.034 5.106 writeSigGeneSet 4.145 0.031 5.067 * 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-3.19-bioc/meat/SeqGSEA.Rcheck/00check.log’ for details.