############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:frmaTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings frmaTools_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/frmaTools.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘frmaTools/DESCRIPTION’ ... OK * this is package ‘frmaTools’ 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 ... NOTE Found the following hidden files and directories: inst/VectorPkg-template/data/.dummy.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘frmaTools’ 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 ... NOTE 'library' or 'require' call to ‘oligo’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘affy’ 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 convertPlatform: no visible global function definition for ‘cleancdfname’ convertPlatform: no visible global function definition for ‘cdfName’ convertPlatform: no visible global function definition for ‘probeNames’ convertPlatform: no visible global function definition for ‘pmindex’ getFidMetaProbesetCore: no visible global function definition for ‘db’ getFidMetaProbesetExtended: no visible global function definition for ‘db’ getFidMetaProbesetFull: no visible global function definition for ‘db’ getFidProbeset: no visible global function definition for ‘db’ makeMaps: no visible global function definition for ‘xy2indices’ makeVectorsAffyBatch: no visible global function definition for ‘ReadAffy’ makeVectorsAffyBatch: no visible global function definition for ‘bg.correct.rma’ makeVectorsAffyBatch: no visible global function definition for ‘pm’ makeVectorsAffyBatch: no visible global function definition for ‘probeNames’ makeVectorsAffyBatch: no visible global function definition for ‘pmindex’ makeVectorsAffyBatch: no visible global function definition for ‘packageVersion’ makeVectorsFeatureSet: no visible global function definition for ‘read.celfiles’ makeVectorsFeatureSet: no visible global function definition for ‘backgroundCorrect’ Undefined global functions or variables: ReadAffy backgroundCorrect bg.correct.rma cdfName cleancdfname db packageVersion pm pmindex probeNames read.celfiles xy2indices Consider adding importFrom("utils", "packageVersion") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed convertPlatform 7.188 0.257 7.452 * 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-3.13-bioc/meat/frmaTools.Rcheck/00check.log’ for details.