############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:broadSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings broadSeq_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/broadSeq.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘broadSeq/DESCRIPTION’ ... OK * this is package ‘broadSeq’ version ‘1.1.0’ * package encoding: UTF-8 * 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 ‘broadSeq’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocStyle’ 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 genes_plot: warning in facet(facet.by, scale = "free"): partial argument match of 'scale' to 'scales' volcanoPlot: warning in ggscatter(x = lFCName, y = "padj", color = "Significant", palette = palette, title = "Volcano plot", label = labelName, repel = TRUE, label.rectangle = TRUE, show.legend = FALSE, label.select = selectedLabel): partial argument match of 'show.legend' to 'show.legend.text' assay_plot: no visible global function definition for ‘ggarrange’ assay_plot: no visible global function definition for ‘text_grob’ biplotAnyPC: no visible binding for global variable ‘PC’ biplotAnyPC: no visible binding for global variable ‘var_pct’ biplotAnyPC: no visible global function definition for ‘pull’ biplotAnyPC: no visible binding for global variable ‘gene’ biplotAnyPC: no visible global function definition for ‘aes’ biplotAnyPC: no visible global function definition for ‘arrow’ biplotAnyPC: no visible global function definition for ‘unit’ combinedEnrichment: no visible global function definition for ‘keytypes’ extract_topGeneLoadings: no visible global function definition for ‘desc’ extract_topGeneLoadings: no visible global function definition for ‘all_of’ genes_plot: no visible global function definition for ‘rowData’ normalizeEdgerCPM: no visible global function definition for ‘is’ plotAnyPC: no visible binding for global variable ‘PC’ plotAnyPC: no visible binding for global variable ‘var_pct’ plotHeatmapCluster: no visible global function definition for ‘is’ plotHeatmapCluster: no visible global function definition for ‘colData’ plotHeatmapCluster: no visible global function definition for ‘rowData’ plotHeatmapCluster: no visible global function definition for ‘all_of’ plot_MDS: no visible global function definition for ‘is’ plot_MDS: no visible global function definition for ‘dist’ plot_MDS: no visible global function definition for ‘cmdscale’ plot_MDS: no visible global function definition for ‘colData’ prcompTidy: no visible global function definition for ‘is’ prcompTidy: no visible global function definition for ‘prcomp’ prcompTidy: no visible binding for global variable ‘stdev’ prcompTidy: no visible binding for global variable ‘var’ prcompTidy: no visible binding for global variable ‘var_pct’ prcompTidy: no visible binding for global variable ‘PC’ prcompTidy: no visible binding for global variable ‘.’ prcompTidy: no visible binding for global variable ‘gene’ transformDESeq2: no visible global function definition for ‘is’ transformDESeq2: no visible global function definition for ‘assays<-’ transformDESeq2: no visible global function definition for ‘assay’ use_DELocal: no visible global function definition for ‘desc’ use_DELocal: no visible binding for global variable ‘relative.logFC’ use_EBSeq: no visible global function definition for ‘desc’ use_EBSeq: no visible binding for global variable ‘PPDE’ use_NOIseq: no visible global function definition for ‘desc’ use_NOIseq: no visible binding for global variable ‘prob’ use_SAMseq: no visible binding for global variable ‘q-value(%)’ use_deseq2: no visible binding for global variable ‘padj’ use_edgeR: no visible binding for global variable ‘logFC’ use_edgeR: no visible binding for global variable ‘FDR’ use_edgeR: no visible global function definition for ‘:=’ use_limma: no visible global function definition for ‘par’ use_limma: no visible binding for global variable ‘logFC’ use_limma: no visible binding for global variable ‘B’ use_limma: no visible global function definition for ‘:=’ volcanoPlot: no visible global function definition for ‘labs’ volcanoPlot: no visible global function definition for ‘geom_abline’ Undefined global functions or variables: . := B FDR PC PPDE aes all_of arrow assay assays<- cmdscale colData desc dist gene geom_abline ggarrange is keytypes labs logFC padj par prcomp prob pull q-value(%) relative.logFC rowData stdev text_grob unit var var_pct Consider adding importFrom("graphics", "par") importFrom("methods", "is") importFrom("stats", "cmdscale", "dist", "prcomp", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: genes_plot.Rd: SummarizedExperiment, ggboxplot normalizeEdgerCPM.Rd: SummarizedExperiment, normLibSizes, cpm plotHeatmapCluster.Rd: SummarizedExperiment, pheatmap plot_MDS.Rd: SummarizedExperiment, ggscatter prcompTidy.Rd: SummarizedExperiment, ggscatter sampleAssay_plot.Rd: SummarizedExperiment, ggboxplot transformDESeq2.Rd: SummarizedExperiment, varianceStabilizingTransformation, normTransform, rlog use_DELocal.Rd: SummarizedExperiment, DELocal use_EBSeq.Rd: SummarizedExperiment, GetDEResults use_NOIseq.Rd: noiseqbio, SummarizedExperiment use_SAMseq.Rd: SummarizedExperiment use_deseq2.Rd: SummarizedExperiment, results, DESeqResults use_edgeR.Rd: SummarizedExperiment, glmLRT, exactTest, topTags use_limma.Rd: SummarizedExperiment use_multDE.Rd: SummarizedExperiment Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 use_multDE 7.477 0.052 7.529 sampleAssay_plot 7.187 0.182 7.370 plot_MDS 5.135 0.037 5.173 * 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-3.21-bioc/meat/broadSeq.Rcheck/00check.log’ for details.