############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wateRmelon_2.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/wateRmelon.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wateRmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wateRmelon’ version ‘2.6.0’ * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: 1.19.1 Updated normalization methods to account for change in minfi MethylSet structure and methods will return 'MethylSet' instead of beta matrix. Cannot process chunk/lines: 1.3.1 Changed annotation method for tost() (minfi and methylumi methods. thanks to several users for bug reports! Cannot process chunk/lines: 0.99.16 replaced dependency on ROCR with ROC (bioconductor) package seabird() no longer takes a vector for the stop argument Cannot process chunk/lines: 0.99.15 codoc corrections. temporarily removed dependency on ROCR (and thus gdata) Cannot process chunk/lines: 0.99.14 MethylSet methods [dn]a[st]e[nt] now return objects containing normalized intensities as well as betas fixed a bug in as.methylumi Cannot process chunk/lines: 0.99.13 fixed swan wrapper generic and MethyLumiSet method bugs Cannot process chunk/lines: 0.99.12 methods d**** now have ... argument so that data without Sentrix IDs should work (thanks to Elodie Portales-Casamar for bug report). Cannot process chunk/lines: 0.99.11 RGChannelSetExtended pfilter method bug fixed Cannot process chunk/lines: 0.99.10 BioConductor submission Cannot process chunk/lines: 0.9.8 MethyLumiSet methods now update history slot new MethyLumiSet method for pfilter RGtoy2 removed from data(minfitoy). This is because minfi now expects the manifest to be a package. swan function patched so that it can process subsets of array data (provided by Jovana Maksimovic). Now works with melon data set. as.methylumi generic function added. Gets fData from package:IlluminaHumanMethylation450k.db . The MethyLumiSet method is useful for ensuring methylumi objects contain this data. Andrew Teschendorff's BMIQ function and a MethyLumiSet method added minfi 1.4.0 has a changed manifest structure resulting in SNP probes being left out of the MethylSet. This breaks genki() for the minfi objects and also the minfitoy data() set. * 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:::.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 9.842 0.136 9.989 seabi 9.070 0.023 9.099 metrics 5.891 0.205 6.102 * 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-3.17-bioc/meat/wateRmelon.Rcheck/00check.log’ for details.