############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings wateRmelon_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/wateRmelon.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘wateRmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wateRmelon’ version ‘2.4.0’ * 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 ... OK * 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 loading without being on the library search path ... 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:::.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 .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 ‘pval.detect<-’ 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’ 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’ estimateSex: no visible binding for global variable ‘sex_coef’ estimateSex: no visible global function definition for ‘colSds’ 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<-’ 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’ readEPIC: no visible binding for global variable ‘n.sd’ sort_order: no visible binding for global variable ‘i’ sort_order: no visible binding for global variable ‘n_1’ 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 binding for global variable ‘ds’ 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,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’ 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’ 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: .mclapply IlluminaHumanMethylation450kanno.ilmn12.hg19 MethylSet PATH_RES QCdata QCdata<- RGChannelSetExtended addSex assay<- assays betas betas<- colCummaxs colData colMeans2 colMedians colQuantiles colSds detectionP ds epic.controls epic.ordering getAnnotation getAnnotationObject getBeta getCN getControlAddress getGreen getManifest getManifestInfo getMeth getNBeads getOOB getProbeInfo getProbeType getRed getSex getSnpBeta getUnmeth hm27.controls hm27.ordering hm450.controls hm450.ordering i intensitiesByChannel mapToGenome mclapply metadata methylated methylated<- methylumiR n.sd n_1 preprocessNoob preprocessRaw preprocessSWAN probeAnnotationsCategory projectName pval.detect<- pvals rowMeans2 seqnames sex_coef 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sextest 6.229 0.072 6.301 seabi 5.398 0.111 5.511 metrics 4.948 0.212 5.160 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘wateRmelon.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/wateRmelon.Rcheck/00check.log’ for details.