############################################################################## ############################################################################## ### ### 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_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SeqGSEA.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SeqGSEA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SeqGSEA’ version ‘1.45.0’ * 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 11.853 0.082 12.005 DENBStatPermut4GSEA 11.430 0.081 11.585 DEpermutePval 11.220 0.109 11.384 DSpermutePval 6.151 0.121 6.302 normFactor 6.078 0.116 6.233 topDSExons 5.787 0.164 6.009 topDSGenes 5.794 0.097 5.942 DSresultExonTable 5.747 0.111 5.891 scoreNormalization 5.716 0.136 5.917 DSpermute4GSEA 5.553 0.206 5.815 DSresultGeneTable 5.493 0.115 5.639 genpermuteMat 5.284 0.167 5.501 * 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/SeqGSEA.Rcheck/00check.log’ for details.