############################################################################## ############################################################################## ### ### 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MAGAR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MAGAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MAGAR’ version ‘1.14.0’ * 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 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 ... NOTE Namespace in Imports field not imported from: ‘RnBeads.hg38’ All declared Imports should be used. * 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 global function definition for ‘after_stat’ 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 global function definition for ‘after_stat’ 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: Annotation Beta CpG Distance GRanges IRanges OddsRatio P.value PC1 PC2 Representative Rle SNP SNPDosage Size Substitution Type aes aes_string after_stat 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 13.263 13.985 53.743 doMethQTLChromosome 11.174 10.573 23.925 computeCorrelationBlocks 4.715 6.199 30.181 imputeMeth 0.298 1.067 11.345 qtlAnnotationEnrichment 1.193 0.060 60.543 qtlVennPlot 0.138 0.181 46.333 qtlManhattanPlot 0.040 0.006 6.719 filterPval 0.019 0.003 27.444 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MAGAR.Rcheck/00check.log’ for details.