############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings hipathia_3.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/hipathia.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 4.5Mb * 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 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 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 25.840 2.016 29.020 create_report 20.471 1.304 22.253 get_pathways_annotations 19.282 1.200 20.980 hipathia 18.876 1.044 20.240 normalize_data 17.873 1.755 19.939 visualize_report 17.715 1.460 19.484 node_color 17.703 1.001 18.981 translate_data 16.986 1.456 18.739 load_pathways 17.184 1.032 18.576 get_pathways_summary 16.769 1.040 18.099 node_color_per_de 16.767 0.912 17.967 get_pathways_list 16.841 0.792 17.890 get_path_names 16.212 0.905 17.395 save_results 16.404 0.652 17.320 pathway_comparison_plot 16.472 0.576 17.357 get_node_names 15.967 0.752 16.996 normalize_paths 15.734 0.757 16.777 * 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 ... ‘hipathia-vignette.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/hipathia.Rcheck/00check.log’ for details.