############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings AGDEX_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/AGDEX.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AGDEX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AGDEX’ version ‘1.42.0’ * 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 ‘AGDEX’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Non-standard license specification: GPL Version 2 or later Standardizable: TRUE Standardized license specification: GPL (>= 2) * 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 ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘GSEABase’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE agdex: no visible global function definition for ‘exprs’ agdex: no visible global function definition for ‘qnorm’ agdex: no visible global function definition for ‘pnorm’ agdex: no visible global function definition for ‘sampleNames’ agdex: no visible global function definition for ‘pData’ agdex.scatterplot: no visible global function definition for ‘points’ agdex.scatterplot: no visible global function definition for ‘lines’ agdex.scatterplot: no visible global function definition for ‘prcomp’ agdex.scatterplot: no visible global function definition for ‘abline’ gsc.to.index.list: no visible global function definition for ‘geneIds’ prep.dex.set: no visible global function definition for ‘exprs’ prep.dex.set: no visible global function definition for ‘pData’ read.agdex.gset.details: no visible global function definition for ‘read.table’ read.agdex.gset.list: no visible global function definition for ‘read.table’ read.agdex.result: no visible global function definition for ‘read.table’ read.enrich.gset.list: no visible global function definition for ‘read.table’ read.gset.collection: no visible global function definition for ‘read.table’ read.gset.collection: no visible global function definition for ‘GeneSet’ read.gset.collection: no visible global function definition for ‘geneIds<-’ read.gset.collection: no visible global function definition for ‘GeneSetCollection’ write.agdex.gset.details: no visible global function definition for ‘write.table’ write.agdex.result: no visible global function definition for ‘write.table’ write.gset.list.result: no visible global function definition for ‘write.table’ Undefined global functions or variables: GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData pnorm points prcomp qnorm read.table sampleNames write.table Consider adding importFrom("graphics", "abline", "lines", "points") importFrom("stats", "pnorm", "prcomp", "qnorm") 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/AGDEX.Rcheck/00check.log’ for details.