################################################################################################################################################################## Running command:###### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEDIPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEDIPS_1.62.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MEDIPS.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘MEDIPS/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘MEDIPS’ version ‘1.62.0’* 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 for sufficient/correct file permissions ... OK* checking whether package ‘MEDIPS’ can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* 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 ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEMEDIPS.CpGenrich: no visible global function definition for ‘seqlevels’MEDIPS.CpGenrich: no visible global function definition for ‘seqlengths’MEDIPS.CpGenrich: no visible global function definition for ‘GRangesList’MEDIPS.CpGenrich : <anonymous>: no visible global function definition for ‘seqnames’MEDIPS.CpGenrich: no visible global function definition for ‘new’MEDIPS.addCNV: no visible global function definition for ‘seqnames’MEDIPS.correlation: no visible global function definition for ‘pdf’MEDIPS.correlation: no visible global function definition for ‘dev.off’MEDIPS.couplingVector: no visible global function definition for ‘new’MEDIPS.createROIset: no visible global function definition for ‘seqnames’MEDIPS.createROIset: no visible global function definition for ‘seqlengths’MEDIPS.createROIset: no visible global function definition for ‘new’MEDIPS.createSet: no visible global function definition for ‘seqnames’MEDIPS.createSet: no visible global function definition for ‘seqlengths’MEDIPS.createSet: no visible global function definition for ‘seqlevels’MEDIPS.createSet: no visible global function definition for ‘new’MEDIPS.diffMeth: no visible global function definition for ‘p.adjust’MEDIPS.exportWIG: no visible global function definition for ‘seqnames’MEDIPS.mergeSets: no visible global function definition for ‘new’MEDIPS.meth: no visible global function definition for ‘seqnames’MEDIPS.plotCalibrationPlot: no visible global function definition for ‘seqnames’MEDIPS.plotCalibrationPlot: no visible global function definition for ‘points’MEDIPS.plotSeqCoverage: no visible global function definition for ‘pie’MEDIPS.plotSeqCoverage: no visible global function definition for ‘hist’MEDIPS.saturation: no visible global function definition for ‘seqlevels’MEDIPS.saturation: no visible global function definition for ‘seqlengths’MEDIPS.selectROIs: no visible global function definition for ‘elementMetadata<-’MEDIPS.selectROIs: no visible global function definition for ‘elementMetadata’MEDIPS.selectROIs: no visible global function definition for ‘findOverlaps’MEDIPS.selectROIs: no visible global function definition for ‘values’MEDIPS.selectROIs: no visible global function definition for ‘seqnames’MEDIPS.seqCoverage: no visible global function definition for ‘seqlevels’MEDIPS.seqCoverage: no visible global function definition for ‘seqlengths’MEDIPS.setAnnotation: no visible global function definition for ‘findOverlaps’MEDIPS.setAnnotation: no visible global function definition for ‘values’getGRange: no visible global function definition for ‘qpois’getGRange: no visible global function definition for ‘seqlengths’getGRange: no visible global function definition for ‘countMatches’getGRange: no visible global function definition for ‘strand<-’getMObjectFromWIG: no visible global function definition for ‘seqlengths’getMObjectFromWIG: no visible global function definition for ‘values’getMObjectFromWIG: no visible global function definition for ‘runLength’getMObjectFromWIG: no visible global function definition for ‘seqnames’getMObjectFromWIG: no visible global function definition for ‘runValue’getMObjectFromWIG: no visible global function definition for ‘new’getPairedGRange: no visible global function definition for ‘sd’getPairedGRange: no visible global function definition for ‘qpois’getPairedGRange: no visible global function definition for ‘seqlengths’getPairedGRange: no visible global function definition for ‘countMatches’getPairedGRange: no visible global function definition for ‘strand<-’matSd: no visible binding for global variable ‘sd’matTtest: no visible binding for global variable ‘sd’matTtest: no visible global function definition for ‘pt’Undefined global functions or variables: GRangesList countMatches dev.off elementMetadata elementMetadata<- findOverlaps hist new p.adjust pdf pie points pt qpois runLength runValue sd seqlengths seqlevels seqnames strand<- valuesConsider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "hist", "pie", "points") importFrom("methods", "new") importFrom("stats", "p.adjust", "pt", "qpois", "sd")to your NAMESPACE file (and ensure that your DESCRIPTION Imports fieldcontains 'methods').* 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 sizes of PDF files under ‘inst/doc’ ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s user system elapsedMEDIPS.meth 42.291 1.832 62.736MEDIPS.addCNV 25.423 0.561 36.380MEDIPS.plotSaturation 9.150 0.587 13.584MEDIPS.saturation 8.548 0.539 12.495MEDIPS.couplingVector 4.892 0.130 6.827MEDIPS.seqCoverage 4.430 0.225 6.367MEDIPS.plotSeqCoverage 4.462 0.179 6.486MEDIPS.plotCalibrationPlot 4.031 0.296 5.986* 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* DONEStatus: 1 NOTESee ‘/Users/biocbuild/bbs-3.22-bioc/meat/MEDIPS.Rcheck/00check.log’for details.################################################################################################################################################################## Running command:###### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MEDIPS###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘MEDIPS’ ...** this is package ‘MEDIPS’ version ‘1.62.0’** using staged installation** R** inst** byte-compile and prepare package for lazy loadingNo methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary locationNo methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’** testing if installed package can be loaded from final locationNo methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’** testing if installed package keeps a record of temporary installation path* DONE (MEDIPS)
