############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings wateRmelon_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/wateRmelon.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wateRmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wateRmelon’ version ‘1.36.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC', 'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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: .git_fetch_output.txt .git_merge_output.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 ‘wateRmelon’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields. * 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: ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘matrixStats’ ‘methylumi’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘minfi:::.isRGOrStop’ ‘minfi:::pickCompProbes’ ‘minfi:::projectCellType’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE IDATsToMatrices2: no visible global function definition for ‘.mclapply’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘betas’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘methylated’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘unmethylated’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘pval.detect<-’ beadcount: no visible global function definition for ‘getNBeads’ beadcount: no visible global function definition for ‘getProbeInfo’ beadcount: no visible global function definition for ‘getManifestInfo’ bgIntensitySwan.methylumi: no visible global function definition for ‘colMedians’ bscon_methy: no visible global function definition for ‘intensitiesByChannel’ bscon_methy: no visible global function definition for ‘QCdata’ bscon_minfi : csp.green: no visible global function definition for ‘getRed’ bscon_minfi : csp.green: no visible global function definition for ‘getGreen’ bscon_minfi : csp.green : : no visible global function definition for ‘getControlAddress’ bscon_minfi : csp.red: no visible global function definition for ‘getRed’ bscon_minfi : csp.red: no visible global function definition for ‘getGreen’ bscon_minfi : csp.red : : no visible global function definition for ‘getControlAddress’ combo : : no visible global function definition for ‘QCdata’ combo: no visible global function definition for ‘QCdata<-’ dfort: no visible binding for global variable ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ estimateCellCounts.wmln: no visible global function definition for ‘colData’ estimateCellCounts.wmln: no visible global function definition for ‘methylated’ estimateCellCounts.wmln: no visible global function definition for ‘unmethylated’ estimateCellCounts.wmln: no visible global function definition for ‘betas’ estimateCellCounts.wmln: no visible global function definition for ‘preprocessRaw’ estimateCellCounts.wmln: no visible global function definition for ‘getProbeType’ estimateCellCounts.wmln: no visible global function definition for ‘getMeth’ estimateCellCounts.wmln: no visible global function definition for ‘getUnmeth’ genall: no visible global function definition for ‘betas’ generateManifest: no visible global function definition for ‘getAnnotationObject’ generateManifest: no visible global function definition for ‘getAnnotation’ generateManifest: no visible global function definition for ‘getProbeInfo’ getMethylationBeadMappers2 : : no visible binding for global variable ‘hm27.ordering’ getMethylationBeadMappers2 : : no visible binding for global variable ‘hm450.ordering’ getMethylationBeadMappers2 : : no visible binding for '<<-' assignment to ‘epic.ordering’ getMethylationBeadMappers2 : : no visible binding for global variable ‘epic.ordering’ getMethylationBeadMappers2 : : no visible binding for global variable ‘hm27.controls’ getMethylationBeadMappers2 : : no visible binding for global variable ‘hm450.controls’ getMethylationBeadMappers2 : : no visible binding for global variable ‘epic.controls’ getMethylumiBeta: no visible global function definition for ‘unmethylated’ getMethylumiBeta: no visible global function definition for ‘methylated’ got: no visible global function definition for ‘getProbeInfo’ lumiMethyR2: no visible global function definition for ‘methylumiR’ oxyscale: no visible global function definition for ‘betas’ oxyscale: no visible global function definition for ‘betas<-’ pipelineIlluminaMethylation.batch: no visible binding for global variable ‘PATH_RES’ pipelineIlluminaMethylation.batch: no visible binding for global variable ‘probeAnnotationsCategory’ predictSex: no visible global function definition for ‘colMedians’ preprocessIlluminaMethylation: no visible binding for global variable ‘projectName’ readEPIC: no visible binding for global variable ‘n.sd’ BMIQ,MethyLumiSet : : no visible global function definition for ‘warn’ BMIQ,MethyLumiSet: no visible global function definition for ‘betas<-’ BMIQ,MethylSet: no visible global function definition for ‘getBeta’ BMIQ,MethylSet : : no visible global function definition for ‘warn’ agep,MethylSet: no visible global function definition for ‘getBeta’ as.methylumi,MethyLumiSet: no visible global function definition for ‘methylated’ as.methylumi,MethyLumiSet: no visible global function definition for ‘unmethylated’ as.methylumi,MethyLumiSet: no visible global function definition for ‘betas’ as.methylumi,MethyLumiSet: no visible global function definition for ‘pvals’ as.methylumi,MethyLumiSet: no visible global function definition for ‘QCdata’ as.methylumi,MethylSet: no visible global function definition for ‘getMeth’ as.methylumi,MethylSet: no visible global function definition for ‘getUnmeth’ as.methylumi,MethylSet: no visible global function definition for ‘getBeta’ as.methylumi,MethylSet: no visible global function definition for ‘getAnnotation’ betaqn,MethyLumiSet: no visible global function definition for ‘betas<-’ betaqn,MethyLumiSet: no visible global function definition for ‘betas’ betaqn,MethylSet: no visible global function definition for ‘getBeta’ betaqn,RGChannelSet: no visible global function definition for ‘getBeta’ colnames,MethyLumiSet: no visible global function definition for ‘methylated’ danen,MethyLumiSet: no visible global function definition for ‘methylated’ danen,MethyLumiSet: no visible global function definition for ‘unmethylated’ danen,MethyLumiSet: no visible global function definition for ‘betas<-’ danen,MethyLumiSet: no visible global function definition for ‘methylated<-’ danen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ danen,MethylSet: no visible global function definition for ‘getMeth’ danen,MethylSet: no visible global function definition for ‘getUnmeth’ danen,MethylSet: no visible global function definition for ‘MethylSet’ danen,MethylSet: no visible global function definition for ‘colData’ danen,MethylSet: no visible global function definition for ‘metadata’ danen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ danes,MethyLumiSet: no visible global function definition for ‘methylated’ danes,MethyLumiSet: no visible global function definition for ‘unmethylated’ danes,MethyLumiSet: no visible global function definition for ‘betas<-’ danes,MethyLumiSet: no visible global function definition for ‘methylated<-’ danes,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ danes,MethylSet: no visible global function definition for ‘getMeth’ danes,MethylSet: no visible global function definition for ‘getUnmeth’ danes,MethylSet: no visible global function definition for ‘MethylSet’ danes,MethylSet: no visible global function definition for ‘colData’ danes,MethylSet: no visible global function definition for ‘metadata’ danes,RGChannelSet: no visible global function definition for ‘preprocessRaw’ danet,MethyLumiSet: no visible global function definition for ‘methylated’ danet,MethyLumiSet: no visible global function definition for ‘unmethylated’ danet,MethyLumiSet: no visible global function definition for ‘betas<-’ danet,MethyLumiSet: no visible global function definition for ‘methylated<-’ danet,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ danet,MethylSet: no visible global function definition for ‘getMeth’ danet,MethylSet: no visible global function definition for ‘getUnmeth’ danet,MethylSet: no visible global function definition for ‘MethylSet’ danet,MethylSet: no visible global function definition for ‘colData’ danet,MethylSet: no visible global function definition for ‘metadata’ danet,RGChannelSet: no visible global function definition for ‘preprocessRaw’ dasen,MethyLumiSet: no visible global function definition for ‘methylated’ dasen,MethyLumiSet: no visible global function definition for ‘unmethylated’ dasen,MethyLumiSet: no visible global function definition for ‘betas<-’ dasen,MethyLumiSet: no visible global function definition for ‘methylated<-’ dasen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ dasen,MethylSet: no visible global function definition for ‘getMeth’ dasen,MethylSet: no visible global function definition for ‘getUnmeth’ dasen,MethylSet: no visible global function definition for ‘MethylSet’ dasen,MethylSet: no visible global function definition for ‘colData’ dasen,MethylSet: no visible global function definition for ‘metadata’ dasen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ daten1,MethyLumiSet: no visible global function definition for ‘methylated’ daten1,MethyLumiSet: no visible global function definition for ‘unmethylated’ daten1,MethyLumiSet: no visible global function definition for ‘betas<-’ daten1,MethyLumiSet: no visible global function definition for ‘methylated<-’ daten1,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ daten1,MethylSet: no visible global function definition for ‘getMeth’ daten1,MethylSet: no visible global function definition for ‘getUnmeth’ daten1,MethylSet: no visible global function definition for ‘MethylSet’ daten1,MethylSet: no visible global function definition for ‘colData’ daten1,MethylSet: no visible global function definition for ‘metadata’ daten1,RGChannelSet: no visible global function definition for ‘preprocessRaw’ daten2,MethyLumiSet: no visible global function definition for ‘methylated’ daten2,MethyLumiSet: no visible global function definition for ‘unmethylated’ daten2,MethyLumiSet: no visible global function definition for ‘betas<-’ daten2,MethyLumiSet: no visible global function definition for ‘methylated<-’ daten2,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ daten2,MethylSet: no visible global function definition for ‘getMeth’ daten2,MethylSet: no visible global function definition for ‘getUnmeth’ daten2,MethylSet: no visible global function definition for ‘MethylSet’ daten2,MethylSet: no visible global function definition for ‘colData’ daten2,MethylSet: no visible global function definition for ‘metadata’ daten2,RGChannelSet: no visible global function definition for ‘preprocessRaw’ dmrse,MethylSet: no visible global function definition for ‘getBeta’ dmrse,RGChannelSet: no visible global function definition for ‘getBeta’ dmrse_col,MethylSet: no visible global function definition for ‘getBeta’ dmrse_col,RGChannelSet: no visible global function definition for ‘getBeta’ dmrse_row,MethylSet: no visible global function definition for ‘getBeta’ dmrse_row,RGChannelSet: no visible global function definition for ‘getBeta’ fuks,MethyLumiSet: no visible global function definition for ‘betas<-’ fuks,MethyLumiSet: no visible global function definition for ‘betas’ fuks,MethylSet: no visible global function definition for ‘getBeta’ fuks,RGChannelSet: no visible global function definition for ‘preprocessRaw’ fuks,RGChannelSet: no visible global function definition for ‘getBeta’ genki,MethyLumiSet: no visible global function definition for ‘betas’ genki,MethylSet: no visible global function definition for ‘getBeta’ genki,RGChannelSet: no visible global function definition for ‘getSnpBeta’ nanes,MethyLumiSet: no visible global function definition for ‘methylated’ nanes,MethyLumiSet: no visible global function definition for ‘unmethylated’ nanes,MethyLumiSet: no visible global function definition for ‘betas<-’ nanes,MethyLumiSet: no visible global function definition for ‘methylated<-’ nanes,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ nanes,MethylSet: no visible global function definition for ‘getMeth’ nanes,MethylSet: no visible global function definition for ‘getUnmeth’ nanes,MethylSet: no visible global function definition for ‘MethylSet’ nanes,MethylSet: no visible global function definition for ‘colData’ nanes,MethylSet: no visible global function definition for ‘metadata’ nanes,RGChannelSet: no visible global function definition for ‘preprocessRaw’ nanet,MethyLumiSet: no visible global function definition for ‘methylated’ nanet,MethyLumiSet: no visible global function definition for ‘unmethylated’ nanet,MethyLumiSet: no visible global function definition for ‘betas<-’ nanet,MethyLumiSet: no visible global function definition for ‘methylated<-’ nanet,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ nanet,MethylSet: no visible global function definition for ‘getMeth’ nanet,MethylSet: no visible global function definition for ‘getUnmeth’ nanet,MethylSet: no visible global function definition for ‘MethylSet’ nanet,MethylSet: no visible global function definition for ‘colData’ nanet,MethylSet: no visible global function definition for ‘metadata’ nanet,RGChannelSet: no visible global function definition for ‘preprocessRaw’ nasen,MethyLumiSet: no visible global function definition for ‘methylated’ nasen,MethyLumiSet: no visible global function definition for ‘unmethylated’ nasen,MethyLumiSet: no visible global function definition for ‘betas<-’ nasen,MethyLumiSet: no visible global function definition for ‘methylated<-’ nasen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ nasen,MethylSet: no visible global function definition for ‘getMeth’ nasen,MethylSet: no visible global function definition for ‘getUnmeth’ nasen,MethylSet: no visible global function definition for ‘MethylSet’ nasen,MethylSet: no visible global function definition for ‘colData’ nasen,MethylSet: no visible global function definition for ‘metadata’ nasen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ naten,MethyLumiSet: no visible global function definition for ‘methylated’ naten,MethyLumiSet: no visible global function definition for ‘unmethylated’ naten,MethyLumiSet: no visible global function definition for ‘betas<-’ naten,MethyLumiSet: no visible global function definition for ‘methylated<-’ naten,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ naten,MethylSet: no visible global function definition for ‘getMeth’ naten,MethylSet: no visible global function definition for ‘getUnmeth’ naten,MethylSet: no visible global function definition for ‘MethylSet’ naten,MethylSet: no visible global function definition for ‘colData’ naten,MethylSet: no visible global function definition for ‘metadata’ naten,RGChannelSet: no visible global function definition for ‘preprocessRaw’ outlyx,MethyLumiSet: no visible global function definition for ‘betas’ outlyx,MethylSet: no visible global function definition for ‘getBeta’ outlyx,RGChannelSet: no visible global function definition for ‘getBeta’ pfilter,MethyLumiSet: no visible global function definition for ‘betas’ pfilter,MethyLumiSet: no visible global function definition for ‘methylated’ pfilter,MethyLumiSet: no visible global function definition for ‘unmethylated’ pfilter,MethyLumiSet: no visible global function definition for ‘pvals’ pfilter,RGChannelSetExtended: no visible binding for global variable ‘RGChannelSetExtended’ pfilter,RGChannelSetExtended: no visible global function definition for ‘preprocessRaw’ pfilter,RGChannelSetExtended: no visible global function definition for ‘detectionP’ pfilter,RGChannelSetExtended: no visible global function definition for ‘subsetByLoci’ pwod,MethyLumiSet: no visible global function definition for ‘betas’ pwod,MethyLumiSet: no visible global function definition for ‘betas<-’ pwod,MethylSet: no visible global function definition for ‘getBeta’ pwod,RGChannelSet: no visible global function definition for ‘getBeta’ seabi,MethyLumiSet: no visible global function definition for ‘betas’ seabi,MethylSet: no visible global function definition for ‘getBeta’ seabi,RGChannelSet: no visible global function definition for ‘getBeta’ swan,MethyLumiSet: no visible global function definition for ‘methylated’ swan,MethyLumiSet: no visible global function definition for ‘unmethylated’ swan,MethyLumiSet: no visible global function definition for ‘intensitiesByChannel’ swan,MethyLumiSet: no visible global function definition for ‘QCdata’ swan,MethyLumiSet: no visible global function definition for ‘getBeta’ swan,MethyLumiSet: no visible global function definition for ‘getMeth’ swan,MethyLumiSet: no visible global function definition for ‘getUnmeth’ swan,MethyLumiSet: no visible global function definition for ‘betas’ swan,RGChannelSet: no visible global function definition for ‘preprocessSWAN’ tost,MethyLumiSet: no visible global function definition for ‘methylated’ tost,MethyLumiSet: no visible global function definition for ‘betas<-’ tost,MethyLumiSet: no visible global function definition for ‘unmethylated’ tost,MethyLumiSet: no visible global function definition for ‘pvals’ tost,RGChannelSet: no visible global function definition for ‘detectionP’ tost,RGChannelSet: no visible global function definition for ‘preprocessRaw’ tost,RGChannelSet: no visible global function definition for ‘getMeth’ tost,RGChannelSet: no visible global function definition for ‘getUnmeth’ Undefined global functions or variables: .mclapply IlluminaHumanMethylation450kanno.ilmn12.hg19 MethylSet PATH_RES QCdata QCdata<- RGChannelSetExtended betas betas<- colData colMedians detectionP epic.controls epic.ordering getAnnotation getAnnotationObject getBeta getControlAddress getGreen getManifestInfo getMeth getNBeads getProbeInfo getProbeType getRed getSnpBeta getUnmeth hm27.controls hm27.ordering hm450.controls hm450.ordering intensitiesByChannel metadata methylated methylated<- methylumiR n.sd preprocessRaw preprocessSWAN probeAnnotationsCategory projectName pval.detect<- pvals subsetByLoci unmethylated unmethylated<- warn * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sextest 12.469 0.165 12.641 seabi 10.232 0.053 10.291 metrics 6.687 0.352 7.043 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/wateRmelon.Rcheck/00check.log’ for details.