############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGAR_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MAGAR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MAGAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MAGAR’ version ‘1.8.0’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MAGAR’ 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getOverlapUniverse: warning in overlapQTLs(meth.qtl.res = meth.qtl.res, type = type): partial argument match of 'meth.qtl.res' to 'meth.qtl.result.list' doGenoImport: no visible global function definition for ‘makeGRangesFromDataFrame’ doGenoImport: no visible global function definition for ‘seqlevelsStyle<-’ doGenoImport: no visible global function definition for ‘findOverlaps’ doGenoImport: no visible global function definition for ‘ggplot’ doGenoImport: no visible global function definition for ‘aes’ doGenoImport: no visible binding for global variable ‘PC1’ doGenoImport: no visible binding for global variable ‘PC2’ doGenoImport: no visible global function definition for ‘geom_point’ doGenoImport: no visible global function definition for ‘xlab’ doGenoImport: no visible global function definition for ‘ylab’ doGenoImport: no visible global function definition for ‘theme_bw’ doGenoImport: no visible global function definition for ‘theme’ doGenoImport: no visible global function definition for ‘element_blank’ doGenoImport: no visible global function definition for ‘element_text’ doGenoImport: no visible global function definition for ‘element_line’ doGenoImport: no visible global function definition for ‘ggsave’ doGenoImportIDAT: no visible global function definition for ‘featureData’ doGenoImportIDAT: no visible global function definition for ‘featureNames’ doGenoImportIDAT: no visible global function definition for ‘chromosome’ doGenoImportIDAT: no visible global function definition for ‘calls’ doGenoImportIDAT: no visible global function definition for ‘makeGRangesFromDataFrame’ doGenoImportIDAT: no visible global function definition for ‘GRanges’ doGenoImportIDAT: no visible global function definition for ‘Rle’ doGenoImportIDAT: no visible global function definition for ‘IRanges’ doGenoImportIDAT: no visible global function definition for ‘findOverlaps’ doGenoImportIDAT: no visible global function definition for ‘queryHits’ doGenoImportIDAT: no visible global function definition for ‘subjectHits’ doGenoImportImputed: no visible global function definition for ‘ggplot’ doGenoImportImputed: no visible global function definition for ‘aes’ doGenoImportImputed: no visible binding for global variable ‘PC1’ doGenoImportImputed: no visible binding for global variable ‘PC2’ doGenoImportImputed: no visible global function definition for ‘geom_point’ doGenoImportImputed: no visible global function definition for ‘xlab’ doGenoImportImputed: no visible global function definition for ‘ylab’ doGenoImportImputed: no visible global function definition for ‘theme_bw’ doGenoImportImputed: no visible global function definition for ‘theme’ doGenoImportImputed: no visible global function definition for ‘element_blank’ doGenoImportImputed: no visible global function definition for ‘element_text’ doGenoImportImputed: no visible global function definition for ‘element_line’ doGenoImportImputed: no visible global function definition for ‘ggsave’ doImport: no visible binding for global variable ‘anno’ doMethImport: no visible global function definition for ‘GRanges’ doMethImport: no visible global function definition for ‘Rle’ doMethImport: no visible global function definition for ‘IRanges’ doMethImport: no visible global function definition for ‘makeGRangesFromDataFrame’ doMethImport: no visible global function definition for ‘findOverlaps’ doMethImport: no visible global function definition for ‘queryHits’ doMethQTLChromosome: no visible global function definition for ‘ggplot’ doMethQTLChromosome: no visible global function definition for ‘aes’ doMethQTLChromosome: no visible binding for global variable ‘Size’ doMethQTLChromosome: no visible binding for global variable ‘..count..’ doMethQTLChromosome: no visible global function definition for ‘geom_histogram’ doMethQTLChromosome: no visible global function definition for ‘geom_vline’ doMethQTLChromosome: no visible global function definition for ‘theme_bw’ doMethQTLChromosome: no visible global function definition for ‘theme’ doMethQTLChromosome: no visible global function definition for ‘element_blank’ doMethQTLChromosome: no visible global function definition for ‘element_text’ doMethQTLChromosome: no visible global function definition for ‘element_line’ doMethQTLChromosome: no visible global function definition for ‘ggsave’ doMethQTLChromosome: no visible global function definition for ‘mclapply’ getOverlapUniverse: no visible global function definition for ‘makeGRangesFromDataFrame’ qtlAnnotationEnrichment: no visible global function definition for ‘findOverlaps’ qtlCorrelateCorBlockStat: no visible global function definition for ‘ggplot’ qtlCorrelateCorBlockStat: no visible global function definition for ‘aes_string’ qtlCorrelateCorBlockStat: no visible global function definition for ‘geom_point’ qtlCorrelateCorBlockStat: no visible global function definition for ‘geom_smooth’ qtlCorrelateCorBlockStat: no visible global function definition for ‘ggtitle’ qtlCorrelateCorBlockStat: no visible global function definition for ‘ylab’ qtlDistanceScatterplot: no visible global function definition for ‘ggplot’ qtlDistanceScatterplot: no visible global function definition for ‘aes’ qtlDistanceScatterplot: no visible binding for global variable ‘Distance’ qtlDistanceScatterplot: no visible binding for global variable ‘P.value’ qtlDistanceScatterplot: no visible global function definition for ‘geom_point’ qtlDistanceScatterplot: no visible global function definition for ‘ggtitle’ qtlDistanceScatterplot: no visible global function definition for ‘xlab’ qtlDistanceScatterplot: no visible global function definition for ‘ylab’ qtlDistanceScatterplot: no visible binding for global variable ‘Beta’ qtlDistanceScatterplot: no visible global function definition for ‘labs’ qtlDistanceScatterplot: no visible global function definition for ‘scale_color_gradient2’ qtlDistanceScatterplot: no visible global function definition for ‘scale_color_continuous’ qtlDistanceScatterplot: no visible global function definition for ‘annotate’ qtlDistanceScatterplot: no visible global function definition for ‘ggsave’ qtlLOLAEnrichment: no visible global function definition for ‘loadRegionDB’ qtlLOLAEnrichment: no visible global function definition for ‘runLOLA’ qtlPlotAnnotationEnrichment: no visible global function definition for ‘ggplot’ qtlPlotAnnotationEnrichment: no visible global function definition for ‘aes’ qtlPlotAnnotationEnrichment: no visible binding for global variable ‘Type’ qtlPlotAnnotationEnrichment: no visible binding for global variable ‘Annotation’ qtlPlotAnnotationEnrichment: no visible binding for global variable ‘OddsRatio’ qtlPlotAnnotationEnrichment: no visible global function definition for ‘geom_tile’ qtlPlotAnnotationEnrichment: no visible global function definition for ‘scale_fill_gradient2’ qtlPlotBaseSubstitution: no visible global function definition for ‘ggplot’ qtlPlotBaseSubstitution: no visible global function definition for ‘aes’ qtlPlotBaseSubstitution: no visible binding for global variable ‘Substitution’ qtlPlotBaseSubstitution: no visible binding for global variable ‘OddsRatio’ qtlPlotBaseSubstitution: no visible global function definition for ‘geom_tile’ qtlPlotBaseSubstitution: no visible global function definition for ‘scale_fill_gradient2’ qtlPlotClusterSize: no visible global function definition for ‘ggplot’ qtlPlotClusterSize: no visible global function definition for ‘aes’ qtlPlotClusterSize: no visible binding for global variable ‘Size’ qtlPlotClusterSize: no visible binding for global variable ‘..count..’ qtlPlotClusterSize: no visible global function definition for ‘geom_histogram’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘ggplot’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘aes’ qtlPlotSNPCorrelationBlock: no visible binding for global variable ‘SNP’ qtlPlotSNPCorrelationBlock: no visible binding for global variable ‘CpG’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘geom_point’ qtlPlotSNPCorrelationBlock: no visible binding for global variable ‘Representative’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘geom_smooth’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘facet_grid’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘theme’ qtlPlotSNPCorrelationBlock: no visible global function definition for ‘scale_color_manual’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘ggplot’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘aes’ qtlPlotSNPCpGInteraction: no visible binding for global variable ‘SNP’ qtlPlotSNPCpGInteraction: no visible binding for global variable ‘CpG’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘geom_boxplot’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘theme_bw’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘ylab’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘xlab’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘ggsave’ qtlPlotSNPCpGInteraction: no visible binding for global variable ‘SNPDosage’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘geom_point’ qtlPlotSNPCpGInteraction: no visible global function definition for ‘geom_smooth’ Undefined global functions or variables: ..count.. Annotation Beta CpG Distance GRanges IRanges OddsRatio P.value PC1 PC2 Representative Rle SNP SNPDosage Size Substitution Type aes aes_string anno annotate calls chromosome element_blank element_line element_text facet_grid featureData featureNames findOverlaps geom_boxplot geom_histogram geom_point geom_smooth geom_tile geom_vline ggplot ggsave ggtitle labs loadRegionDB makeGRangesFromDataFrame mclapply queryHits runLOLA scale_color_continuous scale_color_gradient2 scale_color_manual scale_fill_gradient2 seqlevelsStyle<- subjectHits theme theme_bw xlab ylab * 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 doMethQTL 11.441 3.569 20.016 doMethQTLChromosome 9.868 2.658 18.550 computeCorrelationBlocks 4.725 1.662 9.258 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MAGAR.Rcheck/00check.log’ for details.