############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings EWCE_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/EWCE.Rcheck’ * using R version 4.5.2 (2025-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘EWCE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EWCE’ version ‘1.18.0’ * 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 ‘EWCE’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) compute_gene_scores.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_gene_scores.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:186-187: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:188-189: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:190-192: Lost braces in \itemize; meant \describe ? * 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 ... NOTE Documented arguments not in \usage in Rd file 'get_exp_data_for_bootstrapped_genes.Rd': ‘full_results’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 controlled_geneset_enrichment 19.525 0.375 20.558 merged_ewce 17.366 1.864 20.252 generate_bootstrap_plots_for_transcriptome 14.650 0.239 16.752 filter_genes_without_1to1_homolog 13.784 0.550 14.327 filter_nonorthologs 12.836 0.302 14.157 generate_bootstrap_plots 11.745 0.424 12.908 sct_normalize 9.047 1.457 10.570 ewce_expression_data 10.021 0.260 10.623 check_ewce_genelist_inputs 9.776 0.192 11.786 bootstrap_enrichment_test 9.395 0.204 9.980 merge_ctd 6.808 0.692 7.807 standardise_ctd 7.149 0.291 7.633 filter_ctd_genes 6.331 0.120 7.278 add_res_to_merging_list 5.140 0.198 7.900 bin_specificity_into_quantiles 5.067 0.127 5.274 merge_sce 4.566 0.533 6.246 fix_bad_mgi_symbols 4.563 0.376 6.864 generate_celltype_data 4.156 0.308 6.336 ctd_to_sce 3.436 0.045 5.331 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’