############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MethylSeekR_1.46.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MethylSeekR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MethylSeekR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MethylSeekR’ version ‘1.46.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 for sufficient/correct file permissions ... 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 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 loading without being on the library search path ... 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 ‘values’ 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 ‘values’ calculateFDRs: no visible global function definition for ‘queryHits’ calculateFDRs: no visible global function definition for ‘values<-’ calculateFDRs : : no visible global function definition for ‘Rle’ calculateFDRs : : no visible global function definition for ‘values’ 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’ plotAlphaDistributionOneChr: no visible global function definition for ‘values’ plotFinalSegmentation: no visible global function definition for ‘values’ plotFinalSegmentation: no visible global function definition for ‘Rle’ plotPMDSegmentation: no visible global function definition for ‘values’ readMethylome: no visible global function definition for ‘values’ removeSNPs: no visible global function definition for ‘queryHits’ savePMDSegments: no visible global function definition for ‘values’ saveUMRLMRSegments: no visible global function definition for ‘values’ segmentUMRsLMRs: no visible global function definition for ‘values’ segmentUMRsLMRs : : no visible global function definition for ‘Rle’ segmentUMRsLMRs : : no visible global function definition for ‘values’ 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 ‘values<-’ segmentUMRsLMRs: no visible global function definition for ‘DataFrame’ segmentUMRsLMRs: no visible global function definition for ‘colorRampPalette’ trainPMDHMM: no visible global function definition for ‘values’ Undefined global functions or variables: DataFrame Rle colorRampPalette nrun predict queryHits runValue subjectHits values values<- 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MethylSeekR-package 42.474 0.981 53.834 plotPMDSegmentation 23.633 0.234 23.868 segmentPMDs 23.266 0.114 23.382 savePMDSegments 22.844 0.186 23.031 calculateFDRs 7.541 0.377 16.971 plotAlphaDistributionOneChr 5.352 0.572 5.925 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MethylSeekR.Rcheck/00check.log’ for details.