############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetMashR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetMashR_1.3.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * 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 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetMashR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetMashR’ version ‘1.3.3’ * 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 ... OK * checking for portable file names ... NOTE Found the following non-portable file paths: MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/PE%2816%3A0_18%3A1%29/inchi_key%2Chmdb_id/json.json MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/TG%2816%3A0_16%3A1_18%3A2%29/inchi_key%2Chmdb_id/json.json MetMashR/tests/testthat/lp/lm/compound/abbrev_chains/TG%2816%3A0_16%3A1_18%3A2%29/inchi_key%2Chmdb_id Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘MetMashR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: extdata 5.6Mb * 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 Namespaces in Imports field not imported from: ‘cowplot’ ‘ggplot2’ 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 .get_limits: no visible global function definition for ‘ggplot_build’ scale_color_Publication: no visible global function definition for ‘discrete_scale’ scale_fill_Publication: no visible global function definition for ‘discrete_scale’ theme_Publication: no visible global function definition for ‘theme’ theme_Publication: no visible global function definition for ‘element_text’ theme_Publication: no visible global function definition for ‘rel’ theme_Publication: no visible global function definition for ‘element_rect’ theme_Publication: no visible global function definition for ‘element_line’ theme_Publication: no visible global function definition for ‘element_blank’ theme_Publication: no visible global function definition for ‘unit’ venn_this: no visible global function definition for ‘aes’ venn_this: no visible global function definition for ‘ggplot’ venn_this: no visible binding for global variable ‘geom_polygon’ venn_this: no visible binding for global variable ‘geom_path’ venn_this: no visible global function definition for ‘geom_text’ venn_this: no visible global function definition for ‘theme_void’ venn_this: no visible global function definition for ‘scale_x_continuous’ venn_this: no visible global function definition for ‘expansion’ venn_this: no visible global function definition for ‘theme’ venn_this: no visible global function definition for ‘coord_fixed’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘ggplot’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘aes’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘geom_bar’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘geom_text’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘coord_cartesian’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘theme’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘element_rect’ chart_plot,annotation_bar_chart-annotation_source: no visible global function definition for ‘element_blank’ chart_plot,annotation_histogram-annotation_source: no visible global function definition for ‘ggplot’ chart_plot,annotation_histogram-annotation_source: no visible global function definition for ‘geom_histogram’ chart_plot,annotation_histogram-annotation_source: no visible global function definition for ‘aes’ chart_plot,annotation_histogram-annotation_source: no visible global function definition for ‘geom_vline’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘ggplot’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘aes’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘geom_bin2d’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘theme’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘unit’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘element_rect’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘xlab’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘ylab’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘element_blank’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘coord_cartesian’ chart_plot,annotation_histogram2d-annotation_source: no visible global function definition for ‘coord_flip’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘ggplot’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘aes’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘geom_bar’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘coord_polar’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘theme_void’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘geom_text’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘position_stack’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘theme’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘unit’ chart_plot,annotation_pie_chart-annotation_source: no visible global function definition for ‘xlim’ Undefined global functions or variables: aes coord_cartesian coord_fixed coord_flip coord_polar discrete_scale element_blank element_line element_rect element_text expansion geom_bar geom_bin2d geom_histogram geom_path geom_polygon geom_text geom_vline ggplot ggplot_build position_stack rel scale_x_continuous theme theme_void unit xlab xlim 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 R/sysdata.rda ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/MetMashR.Rcheck/00check.log’ for details.