############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings EWCE_1.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EWCE.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘EWCE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EWCE’ version ‘1.8.2’ * 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 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed controlled_geneset_enrichment 21.854 1.280 23.310 generate_bootstrap_plots 21.447 1.056 22.519 merged_ewce 20.694 1.758 22.365 generate_bootstrap_plots_for_transcriptome 16.043 0.956 17.037 sct_normalize 14.140 1.579 20.775 filter_nonorthologs 14.846 0.668 15.492 filter_genes_without_1to1_homolog 14.841 0.583 15.392 bootstrap_enrichment_test 11.836 0.788 12.629 ewce_expression_data 11.594 0.861 12.484 check_ewce_genelist_inputs 9.910 0.732 10.700 filter_ctd_genes 8.408 0.442 8.816 standardise_ctd 8.180 0.412 9.222 add_res_to_merging_list 6.877 1.045 8.469 merge_ctd 7.335 0.578 8.045 fix_bad_mgi_symbols 5.755 0.861 6.906 merge_sce 4.836 0.296 5.323 generate_celltype_data 4.598 0.503 5.255 drop_uninformative_genes 4.271 0.702 5.087 * 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 ... ‘EWCE.Rmd’ using ‘UTF-8’... OK ‘extended.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK