############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylSeekR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MethylSeekR_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MethylSeekR.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MethylSeekR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MethylSeekR' version '1.32.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'MethylSeekR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: 'parallel' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 Namespace in Imports field not imported from: 'geneplotter' All declared Imports should be used. Package in Depends field not imported from: 'rtracklayer' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE PMDviterbiSegmentation : : no visible global function definition for 'predict' PMDviterbiSegmentation : : no visible global function definition for 'Rle' PMDviterbiSegmentation : : no visible global function definition for 'runValue' calculateAlphaDistr : : no visible global function definition for 'Rle' calculateFDRs: no visible global function definition for 'queryHits' calculateFDRs : : no visible global function definition for 'Rle' calculateFDRs : : no visible global function definition for 'runValue' createGRangesObjectPMDSegmentation : : no visible global function definition for 'Rle' createGRangesObjectPMDSegmentation : : no visible global function definition for 'nrun' createGRangesObjectPMDSegmentation : : no visible global function definition for 'runValue' plotFinalSegmentation: no visible global function definition for 'Rle' removeSNPs: no visible global function definition for 'queryHits' segmentUMRsLMRs : : no visible global function definition for 'Rle' segmentUMRsLMRs : : no visible global function definition for 'runValue' segmentUMRsLMRs: no visible global function definition for 'queryHits' segmentUMRsLMRs: no visible global function definition for 'subjectHits' segmentUMRsLMRs: no visible global function definition for 'Rle' segmentUMRsLMRs: no visible global function definition for 'DataFrame' segmentUMRsLMRs: no visible global function definition for 'colorRampPalette' Undefined global functions or variables: DataFrame Rle colorRampPalette nrun predict queryHits runValue subjectHits Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "predict") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MethylSeekR-package 66.06 3.76 75.45 segmentPMDs 40.16 1.22 41.39 plotPMDSegmentation 39.20 1.72 40.92 savePMDSegments 37.92 1.41 39.33 plotAlphaDistributionOneChr 11.54 0.14 11.69 calculateFDRs 9.33 0.24 14.77 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MethylSeekR-package 50.79 2.39 58.92 plotPMDSegmentation 34.66 1.08 35.74 savePMDSegments 29.70 0.78 30.49 segmentPMDs 27.86 0.75 28.61 calculateFDRs 9.59 0.25 15.10 plotAlphaDistributionOneChr 5.45 0.14 5.60 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MethylSeekR.Rcheck/00check.log' for details.