############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings EWCE_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/EWCE.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.16.0’ * 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 ? checkRd: (-1) drop_uninformative_genes.Rd:52-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:59-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:62-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:69-74: Lost braces in \itemize; meant \describe ? 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checkRd: (-1) extract_matrix.Rd:113: Lost braces 113 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) extract_matrix.Rd:113: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:126: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:127: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:128-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:135: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:136-138: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:139-140: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:141-142: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:161-164: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:165-168: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:169-172: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:44-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:54-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:57-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:61-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:82: Lost braces 82 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) filter_nonorthologs.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:96: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:97-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:105-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:108-109: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:110-111: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:147-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:151-154: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:155-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:74-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:78-80: Lost braces in \itemize; meant \describe ? 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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 ... ERROR Running examples in ‘EWCE-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: generate_bootstrap_plots > ### Title: Generate bootstrap plots > ### Aliases: generate_bootstrap_plots > > ### ** Examples > > ## Load the single cell data > sct_data <- ewceData::ctd() see ?ewceData and browseVignettes('ewceData') for documentation loading from cache > > ## Set the parameters for the analysis > ## Use 5 bootstrap lists for speed, for publishable analysis use >10000 > reps <- 5 > > ## Load the gene list and get human orthologs > hits <- ewceData::example_genelist() see ?ewceData and browseVignettes('ewceData') for documentation loading from cache > > ## Bootstrap significance test, > ## no control for transcript length or GC content > ## Use pre-computed results to speed up example > full_results <- EWCE::example_bootstrap_results() Loading precomputed example bootstrap results. > > ### Skip this for example purposes > # full_results <- EWCE::bootstrap_enrichment_test( > # sct_data = sct_data, > # hits = hits, > # reps = reps, > # annotLevel = 1, > # sctSpecies = "mouse", > # genelistSpecies = "human" > # ) > > output <- EWCE::generate_bootstrap_plots( + sct_data = sct_data, + hits = hits, + reps = reps, + full_results = full_results, + sctSpecies = "mouse", + genelistSpecies = "human", + annotLevel = 1 + ) Warning: sctSpecies_origin not provided. Setting to 'mouse' by default. Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Standardising sct_data. Aligning celltype names with standardise_ctd format. Checking gene list inputs. 1 celltype(s) remain @ <= 0.05 Resampling random genes. Computing gene scores. Generating bootstrap plot for 1 celltype(s). Error: ! The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0 and is now defunct. ℹ Please use the `rows` argument instead. Backtrace: ▆ 1. └─EWCE::generate_bootstrap_plots(...) 2. └─EWCE:::bootstrap_plot(...) 3. └─ggplot2::facet_grid(facets = facets, scales = scales) 4. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed controlled_geneset_enrichment 20.569 0.396 20.979 filter_nonorthologs 15.134 0.631 15.724 filter_genes_without_1to1_homolog 14.049 0.427 14.442 bootstrap_enrichment_test 11.150 0.339 11.453 ewce_expression_data 10.326 0.319 10.520 check_ewce_genelist_inputs 9.399 0.202 9.465 filter_ctd_genes 6.919 0.072 6.920 fix_bad_mgi_symbols 5.910 0.982 7.079 add_res_to_merging_list 6.213 0.327 6.833 bin_specificity_into_quantiles 5.293 0.213 5.581 bin_columns_into_quantiles 5.247 0.248 5.558 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1. └─EWCE::generate_bootstrap_plots(...) at test-bootstrap_enrichment_test.R:43:9 2. └─EWCE:::bootstrap_plot(...) 3. └─ggplot2::facet_grid(facets = facets, scales = scales) 4. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)") 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) ── Failure ('test-ewce_expression_data.R:144:9'): EWCE expression data creation ── `test6` is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 44 | SKIP 0 | PASS 108 ] Error: Test failures Execution halted * 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 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/EWCE.Rcheck/00check.log’ for details.