############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings hipathia_3.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘hipathia/DESCRIPTION’ ... OK * this is package ‘hipathia’ version ‘3.6.0’ * 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 4.5Mb * 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed quantify_terms 17.979 0.526 19.808 create_report 17.114 0.482 18.029 normalize_data 15.466 0.183 16.014 get_pathways_annotations 14.205 0.499 15.637 translate_data 14.120 0.148 14.598 hipathia 13.688 0.144 14.160 visualize_report 13.147 0.134 13.653 node_color 12.551 0.414 13.317 load_pathways 12.674 0.219 13.227 node_color_per_de 12.747 0.126 13.205 pathway_comparison_plot 12.561 0.135 13.104 get_path_names 12.386 0.245 13.121 normalize_paths 12.374 0.138 12.836 get_pathways_summary 12.010 0.280 12.648 get_node_names 12.103 0.164 12.547 get_pathways_list 12.027 0.158 12.511 save_results 12.040 0.123 12.483 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck/00check.log’ for details.