############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EWCE_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/EWCE.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EWCE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EWCE’ version ‘1.4.0’ * 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 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 32.604 0.726 33.790 filter_genes_without_1to1_homolog 27.614 0.467 28.292 controlled_geneset_enrichment 25.794 1.131 27.285 filter_nonorthologs 26.147 0.381 26.777 generate_bootstrap_plots_for_transcriptome 24.619 0.528 26.364 merge_ctd 22.492 0.428 23.351 generate_bootstrap_plots 20.947 0.399 23.638 ewce_expression_data 20.627 0.540 21.511 bootstrap_enrichment_test 19.822 0.451 20.546 add_res_to_merging_list 19.012 1.237 20.990 check_ewce_genelist_inputs 17.857 0.370 18.489 sct_normalize 17.042 0.313 17.811 standardise_ctd 12.502 0.177 12.815 fix_bad_mgi_symbols 9.928 0.354 10.898 merge_sce 9.614 0.155 9.901 bin_specificity_into_quantiles 8.192 0.213 8.543 bin_columns_into_quantiles 8.077 0.161 8.537 ctd_to_sce 8.010 0.123 8.285 plot_ctd 7.717 0.131 7.975 generate_celltype_data 7.312 0.194 7.956 drop_uninformative_genes 6.579 0.475 7.190 get_celltype_table 6.847 0.168 7.439 merge_two_expfiles 6.247 0.297 6.673 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK