############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miaViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miaViz_1.15.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/miaViz.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘miaViz/DESCRIPTION’ ... OK * this is package ‘miaViz’ version ‘1.15.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 21 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 ‘miaViz’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ ‘ggraph’ A package should be listed in only one of these fields. * 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 .abund_plotter: no visible binding for global variable ‘X’ .abund_plotter: no visible binding for global variable ‘Y’ .abund_plotter_incorporate_metadata: no visible binding for global variable ‘X’ .add_paired_samples: no visible global function definition for ‘across’ .add_paired_samples: no visible binding for global variable ‘colour_by’ .add_paired_samples: no visible binding for global variable ‘count’ .add_paired_samples: no visible binding for global variable ‘X’ .add_signif_to_vector_labels : : no visible global function definition for ‘italic’ .calculate_max_and_min_for_loadings: no visible binding for global variable ‘PC’ .calculate_max_and_min_for_loadings: no visible binding for global variable ‘Value’ .feature_plotter: no visible binding for global variable ‘X’ .feature_plotter: no visible binding for global variable ‘Y’ .get_prevalence_plot_matrix: no visible binding for global variable ‘ID’ .get_series_data: no visible global function definition for ‘rowData<-’ .get_series_data: no visible binding for global variable ‘Y’ .incorporate_rda_vis: no visible global function definition for ‘scores’ .order_abundance_cols: no visible binding for global variable ‘X’ .order_abundance_cols: no visible binding for global variable ‘colour_by’ .order_abundance_cols: no visible binding for global variable ‘Y’ .order_abundance_rows: no visible global function definition for ‘unfactor’ .order_abundance_rows: no visible binding for global variable ‘colour_by’ .order_abundance_rows: no visible binding for global variable ‘Y’ .order_abundance_rows: no visible binding for global variable ‘mean_abundance’ .plot_bar_or_lollipop: no visible binding for global variable ‘Sign’ .plot_bar_or_lollipop: no visible binding for global variable ‘max_scale_abs’ .plot_bar_or_lollipop: no visible binding for global variable ‘max_scale’ .plot_loadings: no visible binding for global variable ‘PC’ .plot_loadings: no visible binding for global variable ‘Feature’ .plot_loadings: no visible binding for global variable ‘Value’ .rda_plotter: no visible binding for global variable ‘color’ .rda_plotter: no visible binding for global variable ‘x’ .rda_plotter: no visible binding for global variable ‘y’ .remove_taxonomic_level_from_labels: no visible binding for global variable ‘TAXONOMY_RANKS’ plotLoadings,SingleCellExperiment: no visible global function definition for ‘reducedDims’ plotLoadings,TreeSummarizedExperiment: no visible global function definition for ‘reducedDims’ Undefined global functions or variables: Feature ID PC Sign TAXONOMY_RANKS Value X Y across color colour_by count italic max_scale max_scale_abs mean_abundance reducedDims rowData<- scores unfactor x y * 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: plotColTile.Rd: retrieveFeatureInfo, retrieveCellInfo plotGraph.Rd: ggtree plotPrevalence.Rd: agglomerate-methods plotTree.Rd: ggtree 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotTree 62.504 1.317 64.165 plotDMN 14.291 0.045 14.393 plotAbundance 13.223 0.343 13.604 plotPrevalence 8.305 0.191 8.518 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/miaViz.Rcheck/00check.log’ for details.