############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EWCE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings EWCE_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/EWCE.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'EWCE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'EWCE' version '1.12.0' * 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 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 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 ? checkRd: (-1) drop_uninformative_genes.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:109-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:111: Lost braces 111 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) drop_uninformative_genes.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:124: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:125: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:126-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:132: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:134-136: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:137-138: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:139-140: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:159-162: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:163-166: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:167-170: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:46-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:59-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:63-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:110: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:111-112: Lost braces in \itemize; meant \describe ? 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 ? checkRd: (-1) generate_celltype_data.Rd:81-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:87-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:91-96: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:131: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:132-133: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:134: Lost braces 134 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) generate_celltype_data.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:147: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:148: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:149-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:155: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:156: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:157-159: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:160-161: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:162-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:182-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:186-189: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:190-193: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:49-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:59-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:62-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:66-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:120: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:121-122: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:123: Lost braces 123 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) standardise_ctd.Rd:123: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:136: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:137: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:138-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:144: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:145: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:146-148: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:149-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:151-152: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:171-174: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:175-178: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:179-182: 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 24.11 2.72 26.99 merged_ewce 24.22 2.46 27.31 generate_bootstrap_plots_for_transcriptome 18.28 1.61 27.72 filter_genes_without_1to1_homolog 15.20 1.19 16.51 bootstrap_enrichment_test 13.30 2.38 16.07 generate_bootstrap_plots 13.34 1.69 17.93 filter_nonorthologs 13.12 0.94 14.14 ewce_expression_data 12.25 1.58 14.47 add_res_to_merging_list 8.52 4.64 29.29 sct_normalize 11.33 1.51 13.06 check_ewce_genelist_inputs 10.92 1.25 12.49 filter_ctd_genes 9.44 1.11 10.63 standardise_ctd 8.86 1.05 10.00 merge_ctd 8.47 1.39 9.94 fix_bad_mgi_symbols 5.49 1.30 8.96 bin_specificity_into_quantiles 5.78 0.71 6.57 merge_sce 5.75 0.64 6.56 drop_uninformative_genes 4.56 0.90 9.25 generate_celltype_data 4.27 0.90 5.25 bin_columns_into_quantiles 4.42 0.71 5.17 ctd_to_sce 4.23 0.71 5.04 fix_bad_hgnc_symbols 1.17 0.51 7.95 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/EWCE.Rcheck/00check.log' for details.