############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hipathia_3.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 33.962 2.083 46.257 normalize_data 25.944 1.125 30.198 create_report 24.840 0.961 29.920 hipathia 24.502 1.013 28.338 get_pathways_annotations 23.618 1.645 30.827 get_pathways_summary 23.522 1.261 27.678 node_color_per_de 23.335 0.821 27.017 node_color 22.725 1.221 27.161 translate_data 23.376 0.279 26.577 get_node_names 21.844 0.622 24.802 get_path_names 21.065 1.219 25.077 pathway_comparison_plot 21.507 0.463 25.009 load_pathways 20.947 0.846 24.611 get_pathways_list 20.357 1.017 23.699 normalize_paths 20.285 0.873 24.397 save_results 19.221 1.524 23.113 visualize_report 20.305 0.363 23.584 get_go_names 3.733 0.619 7.112 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/hipathia.Rcheck/00check.log’ for details.