############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hipathia_3.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/hipathia.Rcheck’ * using R version 4.3.3 (2024-02-29) * 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 Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hipathia/DESCRIPTION’ ... OK * this is package ‘hipathia’ version ‘3.2.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘hipathia’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: data 4.1Mb extdata 4.4Mb * 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 DAreport: no visible binding for global variable ‘ID’ DAreport: no visible binding for global variable ‘FDRp.value’ DAtop : : no visible binding for global variable ‘FDRp.value’ DAtop : : no visible binding for global variable ‘statistic’ DAtop : : no visible binding for global variable ‘p.value’ DAtop : : no visible binding for global variable ‘name’ DAtop : : no visible binding for global variable ‘logPV’ DAtop : : no visible binding for global variable ‘feature’ DAtop: no visible binding for global variable ‘name’ DAtop: no visible binding for global variable ‘logPV’ DAtop: no visible binding for global variable ‘direction’ get_edges_df: no visible binding for global variable ‘from’ get_edges_df: no visible binding for global variable ‘to’ nsig_plot: no visible binding for global variable ‘total’ nsig_plot: no visible binding for global variable ‘UPs’ nsig_plot: no visible binding for global variable ‘DOWNs’ nsig_plot: no visible binding for global variable ‘feature’ nsig_plot: no visible binding for global variable ‘UP’ nsig_plot: no visible binding for global variable ‘DOWN’ nsig_plot: no visible binding for global variable ‘Not’ nsig_plot: no visible binding for global variable ‘value’ nsig_plot: no visible binding for global variable ‘variable’ prepare_DAedges: no visible binding for global variable ‘to’ prepare_DAedges: no visible binding for global variable ‘functional’ prepare_DAedges: no visible binding for global variable ‘status’ prepare_DAedges: no visible binding for global variable ‘type’ prepare_DAnodes : : no visible binding for global variable ‘ID’ prepare_DAnodes : : no visible binding for global variable ‘FDRp.value’ prepare_DAnodes : : no visible binding for global variable ‘statistic’ prepare_DAnodes : : no visible binding for global variable ‘p.value’ prepare_edges: no visible binding for global variable ‘to’ prepare_edges: no visible binding for global variable ‘functional’ summary_plot: no visible binding for global variable ‘total’ summary_plot: no visible binding for global variable ‘UPs’ summary_plot: no visible binding for global variable ‘DOWNs’ summary_plot: no visible binding for global variable ‘name’ summary_plot: no visible binding for global variable ‘UP’ summary_plot: no visible binding for global variable ‘DOWN’ summary_plot: no visible binding for global variable ‘Not’ summary_plot: no visible binding for global variable ‘value’ summary_plot: no visible binding for global variable ‘variable’ summary_plot: no visible binding for global variable ‘UP.nodes’ summary_plot: no visible binding for global variable ‘DOWN.nodes’ summary_plot: no visible binding for global variable ‘nodes’ summary_plot: no visible binding for global variable ‘ratio.sigs’ summary_plot: no visible binding for global variable ‘ratio.UPs’ summary_plot: no visible binding for global variable ‘ratio.DOWNs’ Undefined global functions or variables: DOWN DOWN.nodes DOWNs FDRp.value ID Not UP UP.nodes UPs direction feature from functional logPV name nodes p.value ratio.DOWNs ratio.UPs ratio.sigs statistic status to total type value variable * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed quantify_terms 40.847 1.391 46.581 create_report 30.571 0.619 33.311 get_pathways_annotations 29.840 0.756 33.956 hipathia 28.700 0.452 30.543 get_path_names 25.919 0.441 27.674 load_pathways 25.874 0.441 27.470 node_color 25.734 0.404 27.563 get_pathways_summary 25.637 0.447 27.276 get_node_names 25.683 0.399 27.042 node_color_per_de 25.620 0.449 27.496 pathway_comparison_plot 25.562 0.425 27.156 visualize_report 25.489 0.458 27.732 normalize_paths 25.372 0.404 27.187 get_pathways_list 25.054 0.439 26.385 save_results 23.893 0.397 25.169 normalize_data 19.758 0.518 21.414 translate_data 17.223 0.348 18.981 get_go_names 4.662 0.358 6.311 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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-3.18-bioc-mac-arm64/meat/hipathia.Rcheck/00check.log’ for details.