############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings EWCE_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/EWCE.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘EWCE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EWCE’ version ‘1.6.0’ * 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 ‘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 merged_ewce 26.709 0.765 31.976 controlled_geneset_enrichment 22.301 0.320 22.765 filter_nonorthologs 15.821 0.457 16.333 filter_genes_without_1to1_homolog 14.927 0.347 15.317 generate_bootstrap_plots_for_transcriptome 14.222 0.232 14.430 generate_bootstrap_plots 12.046 0.336 12.354 bootstrap_enrichment_test 11.987 0.352 12.346 ewce_expression_data 11.398 0.645 12.029 check_ewce_genelist_inputs 10.990 0.234 11.243 sct_normalize 9.645 0.820 10.558 filter_ctd_genes 7.576 0.320 7.840 standardise_ctd 7.591 0.288 7.870 add_res_to_merging_list 7.601 0.272 8.472 merge_ctd 7.285 0.402 7.787 fix_bad_mgi_symbols 6.206 0.453 6.929 merge_sce 5.464 0.100 5.680 plot_ctd 5.129 0.197 6.106 ctd_to_sce 4.896 0.184 5.211 * 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