############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wateRmelon.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings wateRmelon_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/wateRmelon.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'wateRmelon/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'wateRmelon' version '2.13.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO 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 ... OK * checking for portable file names ... 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 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 ... WARNING '::' or ':::' import not declared from: 'R.utils' 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:::.annoGet' 'minfi:::.availableAnnotation' 'minfi:::.isRGOrStop' 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 readPepo: warning in dir(idatdir, patt = "idat"): partial argument match of 'patt' to 'pattern' .adjusted_normalizeFunnorm450k : unbiased_normalizeQuantiles: no visible global function definition for 'colQuantiles' .adjusted_normalizeFunnorm450k: no visible global function definition for 'getMeth' .adjusted_normalizeFunnorm450k: no visible global function definition for 'getUnmeth' .adjusted_normalizeFunnorm450k: no visible global function definition for 'assay<-' .buildControlMatrix450k: no visible global function definition for 'colMeans2' .extractFromRGSet450k: no visible global function definition for 'getProbeInfo' .extractFromRGSet450k: no visible global function definition for 'getRed' .extractFromRGSet450k: no visible global function definition for 'getGreen' .extractFromRGSet450k: no visible global function definition for 'getOOB' .extractFromRGSet450k: no visible global function definition for 'colQuantiles' .getFunnormIndices: no visible global function definition for 'getProbeType' .getFunnormIndices: no visible global function definition for 'seqnames' .isMatrixBacked: no visible global function definition for 'assays' .regularizeQuantiles: no visible global function definition for 'colCummaxs' .returnFit: no visible global function definition for 'rowMeans2' 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 'pvals<-' adjustedFunnorm: no visible global function definition for 'preprocessNoob' adjustedFunnorm: no visible global function definition for 'mapToGenome' adjustedFunnorm: no visible global function definition for 'addSex' adjustedFunnorm: no visible global function definition for 'getSex' adjustedFunnorm: no visible global function definition for 'getCN' adjustedFunnorm: no visible global function definition for 'assay<-' 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' canno: no visible global function definition for 'IlluminaMethylationManifest' combo : : no visible global function definition for 'QCdata' combo: no visible global function definition for 'QCdata<-' detectP: no visible global function definition for 'QCdata' detectP: no visible global function definition for 'methylated' detectP: no visible global function definition for 'unmethylated' detectP: no visible global function definition for 'colMedians' detectP: no visible global function definition for 'colMads' detectP: no visible global function definition for 'pnorm' dfort: no visible binding for global variable 'IlluminaHumanMethylation450kanno.ilmn12.hg19' epicv2clean.gds.class: no visible global function definition for 'chainsaw' estimateSex: no visible global function definition for 'head' estimateSex: no visible binding for global variable 'sex_coef' estimateSex: no visible global function definition for 'colSds' genall: no visible global function definition for 'head' generateManifest: no visible binding for global variable '.manifest' 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 '<<-' assignment to 'epicV2.ordering' getMethylationBeadMappers2 : : no visible binding for global variable 'epicV2.ordering' getMethylationBeadMappers2 : : no visible binding for global variable '.manifest' 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' getMethylationBeadMappers2 : : no visible binding for global variable 'epicV2.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<-' p_dfsfit: no visible global function definition for 'mclapply' pipelineIlluminaMethylation.batch: no visible binding for global variable 'PATH_RES' pipelineIlluminaMethylation.batch: no visible binding for global variable 'probeAnnotationsCategory' preprocessIlluminaMethylation: no visible binding for global variable 'projectName' read.manifest: no visible global function definition for 'DNAStringSet' read.manifest: no visible global function definition for 'oligonucleotideFrequency' read.manifest: no visible global function definition for 'letterFrequency' readEPIC: no visible binding for global variable 'n.sd' readPepo: no visible binding for '<<-' assignment to '.manifest' uSexQNengine: no visible global function definition for 'mclapply' 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' adjustedDasen,MethyLumiSet: no visible global function definition for 'methylated' adjustedDasen,MethyLumiSet: no visible global function definition for 'unmethylated' adjustedDasen,MethyLumiSet: no visible global function definition for 'betas<-' adjustedDasen,MethyLumiSet: no visible global function definition for 'methylated<-' adjustedDasen,MethyLumiSet: no visible global function definition for 'unmethylated<-' adjustedDasen,MethylSet: no visible global function definition for 'getMeth' adjustedDasen,MethylSet: no visible global function definition for 'getUnmeth' adjustedDasen,MethylSet: no visible global function definition for 'getAnnotation' adjustedDasen,MethylSet: no visible global function definition for 'MethylSet' adjustedDasen,MethylSet: no visible global function definition for 'colData' adjustedDasen,MethylSet: no visible global function definition for 'metadata' adjustedDasen,RGChannelSet: no visible global function definition for 'preprocessRaw' 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,MethylSet: no visible global function definition for 'head' dmrse,RGChannelSet: no visible global function definition for 'getBeta' dmrse,RGChannelSet: no visible global function definition for 'head' dmrse_col,MethylSet: no visible global function definition for 'getBeta' dmrse_col,MethylSet: no visible global function definition for 'head' dmrse_col,RGChannelSet: no visible global function definition for 'getBeta' dmrse_col,RGChannelSet: no visible global function definition for 'head' dmrse_row,MethylSet: no visible global function definition for 'getBeta' dmrse_row,MethylSet: no visible global function definition for 'head' dmrse_row,RGChannelSet: no visible global function definition for 'getBeta' dmrse_row,RGChannelSet: no visible global function definition for 'head' estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for 'getManifest' estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for 'getMeth' estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for 'getUnmeth' estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for 'getBeta' estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for 'getManifest' estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for 'preprocessRaw' estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for 'getMeth' estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for 'getUnmeth' estimateCellCounts.wateRmelon,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' smokp,MethylSet: 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' uSexQN,MethyLumiSet: no visible global function definition for 'methylated' uSexQN,MethyLumiSet: no visible global function definition for 'unmethylated' uSexQN,MethyLumiSet: no visible global function definition for 'betas<-' uSexQN,MethyLumiSet: no visible global function definition for 'methylated<-' uSexQN,MethyLumiSet: no visible global function definition for 'unmethylated<-' uSexQN,MethylSet: no visible global function definition for 'getMeth' uSexQN,MethylSet: no visible global function definition for 'getUnmeth' uSexQN,MethylSet: no visible global function definition for 'getAnnotation' uSexQN,MethylSet: no visible global function definition for 'MethylSet' uSexQN,MethylSet: no visible global function definition for 'colData' uSexQN,MethylSet: no visible global function definition for 'metadata' uSexQN,RGChannelSet: no visible global function definition for 'preprocessRaw' Undefined global functions or variables: .manifest .mclapply DNAStringSet IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaMethylationManifest MethylSet PATH_RES QCdata QCdata<- RGChannelSetExtended addSex assay<- assays betas betas<- chainsaw colCummaxs colData colMads colMeans2 colMedians colQuantiles colSds detectionP epic.controls epic.ordering epicV2.controls epicV2.ordering getAnnotation getAnnotationObject getBeta getCN getControlAddress getGreen getManifest getManifestInfo getMeth getNBeads getOOB getProbeInfo getProbeType getRed getSex getSnpBeta getUnmeth head hm27.controls hm27.ordering hm450.controls hm450.ordering intensitiesByChannel letterFrequency mapToGenome mclapply metadata methylated methylated<- methylumiR n.sd oligonucleotideFrequency pnorm preprocessNoob preprocessRaw preprocessSWAN probeAnnotationsCategory projectName pvals pvals<- rowMeans2 seqnames sex_coef subsetByLoci unmethylated unmethylated<- warn Consider adding importFrom("stats", "pnorm") importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) combo.Rd:24: Lost braces; missing escapes or markup? 24 | and \code{phenoData} are joined on \code{sampleName} . \code{featureData} and {annotation} are taken from | ^ * checking Rd metadata ... WARNING Rd files with duplicated alias 'NChannelSetToMethyLumiSet2': 'NChannelSetToMethyLumiSet2.Rd' 'wm_internal.Rd' Rd files with duplicated alias 'fot': 'dot-getManifestString.Rd' 'got.Rd' Rd files with duplicated alias 'got': 'dot-getManifestString.Rd' 'got.Rd' * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'detectP' Undocumented data sets: 'ageCoefs' 'epicV2.controls' 'sex_coef' Undocumented S4 methods: generic 'adjustedDasen' and siglist 'MethyLumiSet' generic 'adjustedDasen' and siglist 'MethylSet' generic 'adjustedDasen' and siglist 'RGChannelSet' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'readEPIC.Rd': readEPIC Code: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F, n = T, oob = F, force = F, two = TRUE, ...) Docs: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F, n = T, oob = F, force = F, ...) Argument names in code not in docs: two Mismatches in argument names: Position: 8 Code: two Docs: ... * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'canno.Rd' 'name' Undocumented arguments in Rd file 'dot-createAnnotation.Rd' 'object' Documented arguments not in \usage in Rd file 'dot-getManifestString.Rd': 'x' 'obj' 'fd' 'rn' Undocumented arguments in Rd file 'epicv2clean.default.Rd' 'x' Undocumented arguments in Rd file 'readPepo.Rd' 'oob' Documented arguments not in \usage in Rd file 'readPepo.Rd': 'keep' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'read.manifest.Rd': 'file' Argument items with no description in Rd file 'wm_internal.Rd': 'mats' 'chans' 'parallel' 'protocol.data' 'IDAT' 'force' * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed adjustedDasen 23.32 0.92 24.31 sextest 8.29 0.23 8.52 seabi 7.89 0.09 7.98 metrics 5.76 0.28 6.08 * 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: 5 WARNINGs, 4 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/wateRmelon.Rcheck/00check.log' for details.