############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:hypeR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings hypeR_2.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hypeR.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * 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 ‘hypeR/DESCRIPTION’ ... OK * this is package ‘hypeR’ version ‘2.3.0’ * 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 ‘hypeR’ can be installed ... OK * checking installed package size ... OK * 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 ... WARNING '::' or ':::' import not declared from: ‘tibble’ Namespace in Imports field not imported from: ‘BiocStyle’ 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 .dots_multi_plot : : no visible binding for global variable ‘pval’ .dots_multi_plot : : no visible binding for global variable ‘fdr’ .dots_multi_plot : : no visible binding for global variable ‘label’ .dots_multi_plot: no visible global function definition for ‘head’ .dots_multi_plot: no visible binding for global variable ‘.’ .dots_multi_plot: no visible binding for global variable ‘label’ .dots_multi_plot: no visible binding for global variable ‘geneset’ .dots_multi_plot: no visible binding for global variable ‘size’ .dots_multi_plot: no visible binding for global variable ‘overlap’ .dots_multi_plot: no visible binding for global variable ‘significance’ .dots_multi_plot: no visible binding for global variable ‘signature’ .dots_plot: no visible binding for global variable ‘pval’ .dots_plot: no visible binding for global variable ‘fdr’ .dots_plot: no visible binding for global variable ‘significance’ .dots_plot: no visible binding for global variable ‘size’ .enrichment_map: no visible binding for global variable ‘pval’ .enrichment_map: no visible binding for global variable ‘fdr’ .find_members: no visible binding for global variable ‘from’ .find_members: no visible binding for global variable ‘to’ .hiearchy_map: no visible binding for global variable ‘pval’ .hiearchy_map: no visible binding for global variable ‘fdr’ .hiearchy_map : : no visible binding for global variable ‘label’ .hyper_enrichment: no visible global function definition for ‘is’ .ks_enrichment: no visible global function definition for ‘is’ .ks_enrichment: no visible binding for global variable ‘fdr’ .ks_enrichment: no visible binding for global variable ‘pval’ .ks_enrichment: no visible binding for global variable ‘geneset’ .ks_enrichment: no visible binding for global variable ‘label’ enrichr_available: no visible binding for global variable ‘.’ ggvenn: no visible binding for global variable ‘x’ ggvenn: no visible binding for global variable ‘y’ hyp_dots: no visible global function definition for ‘is’ hyp_emap: no visible global function definition for ‘is’ hyp_hmap: no visible global function definition for ‘is’ hyp_show: no visible global function definition for ‘is’ hyp_to_excel: no visible global function definition for ‘is’ hyp_to_graph: no visible global function definition for ‘is’ hyp_to_rmd: no visible global function definition for ‘is’ hyp_to_rmd : : no visible global function definition for ‘is’ hyp_to_table: no visible global function definition for ‘is’ hyp_to_table: no visible global function definition for ‘write.table’ hypeR: no visible global function definition for ‘is’ hypeR: no visible global function definition for ‘packageVersion’ hypeR: no visible global function definition for ‘head’ msigdb_available: no visible binding for global variable ‘gs_cat’ msigdb_available: no visible binding for global variable ‘gs_subcat’ msigdb_download: no visible binding for global variable ‘gs_name’ msigdb_download: no visible binding for global variable ‘gene_symbol’ msigdb_version: no visible global function definition for ‘packageVersion’ rctbl_build: no visible global function definition for ‘is’ Undefined global functions or variables: . fdr from gene_symbol geneset gs_cat gs_name gs_subcat head is label overlap packageVersion pval signature significance size to write.table x y Consider adding importFrom("methods", "is", "signature") importFrom("utils", "head", "packageVersion", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'dot-dots_multi_plot.Rd': .dots_multi_plot Code: function(multihyp_data, top = 20, abrv = 50, size_by = c("genesets", "significance", "overlap", "none"), pval_cutoff = 1, fdr_cutoff = 1, val = c("fdr", "pval"), title = "") Docs: function(multihyp_data, top = 20, abrv = 50, size_by = c("genesets", "significance", "none"), pval_cutoff = 1, fdr_cutoff = 1, val = c("fdr", "pval"), title = "") Mismatches in argument default values: Name: 'size_by' Code: c("genesets", "significance", "overlap", "none") Docs: c("genesets", "significance", "none") * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed msigdb_available 17.618 1.840 19.458 hyp_hmap 4.872 0.188 5.446 enrichr_download 0.058 0.003 11.435 * 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 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/hypeR.Rcheck/00check.log’ for details.