############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:katdetectr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings katdetectr_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/katdetectr.Rcheck’ * using R version 4.5.0 Patched (2025-04-21 r88169) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘katdetectr/DESCRIPTION’ ... OK * this is package ‘katdetectr’ version ‘1.11.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘katdetectr’ 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 ... NOTE .addEmptySegments: no visible binding for global variable ‘seqnames’ .annotateKataegisSegments: no visible binding for global variable ‘fociID’ .annotateKataegisSegments: no visible binding for global variable ‘seqnames’ .annotateKataegisSegments: no visible binding for global variable ‘firstVariantID’ .annotateKataegisSegments: no visible binding for global variable ‘firstVariantOfSeqname’ .annotateKataegisSegments: no visible binding for global variable ‘lastVariantID’ .coerceMAFtoVRanges: no visible binding for global variable ‘start’ .coerceMAFtoVRanges: no visible binding for global variable ‘end’ .convertVariantsToGGplotFormat: no visible binding for global variable ‘IMD’ .convertVariantsToGGplotFormat: no visible binding for global variable ‘variantType’ .determineInitialProbabilities: no visible binding for global variable ‘seqnames’ .determineKataegisSegments: no visible binding for global variable ‘meanIMD’ .determineKataegisSegments: no visible binding for global variable ‘IMDcutoff’ .determineKataegisSegments: no visible binding for global variable ‘seqnames’ .generateBackgroundVariants: no visible binding for global variable ‘seqnames’ .generateBackgroundVariants: no visible binding for global variable ‘mutType’ .generateBackgroundVariants: no visible binding for global variable ‘start’ .generateBackgroundVariants: no visible binding for global variable ‘mutLength’ .generateBackgroundVariants: no visible binding for global variable ‘REF’ .generateKataegisFoci: no visible binding for global variable ‘seqnames’ .generateKataegisFoci: no visible binding for global variable ‘startKataegisFoci’ .generateKataegisVariants: no visible binding for global variable ‘synthFociID’ .generateKataegisVariants: no visible binding for global variable ‘startKataegisFoci’ .generateKataegisVariants: no visible binding for global variable ‘endKataegisFoci’ .generateKataegisVariants: no visible binding for global variable ‘start’ .generateRainfallPlot: no visible binding for global variable ‘variantID’ .generateRainfallPlot: no visible binding for global variable ‘IMD’ .generateRainfallPlot: no visible binding for global variable ‘seqnames’ .generateRainfallPlot: no visible binding for global variable ‘variantType’ .generateRainfallPlot: no visible binding for global variable ‘putativeKataegis’ .generateRainfallPlot: no visible binding for global variable ‘firstVariantID’ .generateRainfallPlot: no visible binding for global variable ‘lastVariantID’ .generateRainfallPlot: no visible binding for global variable ‘meanIMD’ .mergeKataegisSegments: no visible binding for global variable ‘segmentID’ .mergeKataegisSegments: no visible binding for global variable ‘seqnames’ .mergeKataegisSegments: no visible binding for global variable ‘fociID’ .mergeKataegisSegments: no visible binding for global variable ‘start’ .mergeKataegisSegments: no visible binding for global variable ‘end’ .mergeKataegisSegments: no visible binding for global variable ‘sampleNames’ .mergeKataegisSegments: no visible binding for global variable ‘totalVariants’ .mergeKataegisSegments: no visible binding for global variable ‘firstVariantID’ .mergeKataegisSegments: no visible binding for global variable ‘lastVariantID’ .mergeKataegisSegments: no visible binding for global variable ‘meanIMD’ .mergeKataegisSegments: no visible binding for global variable ‘IMDcutoff’ .removeValidationColumns: no visible binding for global variable ‘seqnames’ .removeValidationColumns: no visible binding for global variable ‘start’ .removeValidationColumns: no visible binding for global variable ‘end’ .removeValidationColumns: no visible binding for global variable ‘width’ .removeValidationColumns: no visible binding for global variable ‘strand’ .removeValidationColumns: no visible binding for global variable ‘ref’ .removeValidationColumns: no visible binding for global variable ‘alt’ .removeValidationColumns: no visible binding for global variable ‘totalDepth’ .removeValidationColumns: no visible binding for global variable ‘refDepth’ .removeValidationColumns: no visible binding for global variable ‘altDepth’ .removeValidationColumns: no visible binding for global variable ‘sampleNames’ .selectSequences: no visible binding for global variable ‘seqnames’ determineSegments: no visible binding for global variable ‘sampleNames’ determineSegments: no visible binding for global variable ‘seqnames’ determineSegments: no visible binding for global variable ‘segmentID’ determineSegments: no visible binding for global variable ‘variantID’ determineSegments: no visible binding for global variable ‘start’ determineSegments: no visible binding for global variable ‘IMD’ determineSegments: no visible binding for global variable ‘end’ determineSegments: no visible binding for global variable ‘meanIMD’ determineSegments: no visible binding for global variable ‘totalVariants’ determineSegments: no visible binding for global variable ‘mutationRate’ rainfallPlot: no visible binding for global variable ‘seqnames’ Undefined global functions or variables: IMD IMDcutoff REF alt altDepth end endKataegisFoci firstVariantID firstVariantOfSeqname fociID lastVariantID meanIMD mutLength mutType mutationRate putativeKataegis ref refDepth sampleNames segmentID seqnames start startKataegisFoci strand synthFociID totalDepth totalVariants variantID variantType width Consider adding importFrom("stats", "end", "start") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'rainfallPlot.Rd': ‘[katdetectr]{KatDetect}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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 * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/katdetectr.Rcheck/00check.log’ for details.