############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:orthogene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings orthogene_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthogene.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘orthogene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘orthogene’ version ‘1.11.0’ * 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 ‘orthogene’ 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) aggregate_mapped_genes.Rd:37-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) aggregate_mapped_genes.Rd:41-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) aggregate_mapped_genes.Rd:45-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:16-17: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:18: Lost braces 18 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) check_gene_df_type.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:38: Lost braces 38 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) convert_orthologs.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:54-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:66-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:68-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:101-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:105-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:108-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:114-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:118-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:156-159: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:160-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:164-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:59-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:66-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:72-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:76-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_silhouettes.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_silhouettes.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_silhouettes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_silhouettes.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) gprofiler_namespace.Rd:20: Lost braces 20 | Available namespaces used by link[gprofiler2]{gconvert}. | ^ checkRd: (-1) infer_species.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:26: Lost braces 26 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) infer_species.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:42-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs.Rd:57-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs.Rd:61-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs_custom.Rd:21-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs_custom.Rd:25-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs_custom.Rd:29-32: Lost braces in \itemize; meant \describe ? checkRd: (-1) orthogene-package.Rd:10-11: Lost braces in \itemize; meant \describe ? checkRd: (-1) orthogene-package.Rd:12-13: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:62-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:65-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:72-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:75-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:83-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:87-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:90-92: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:93-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:96-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:100-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:135: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:136: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:137-138: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:141: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:142: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:143: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:144: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) prepare_tree.Rd:28-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:31-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:34-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:38-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:67-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:70-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:73-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:77-82: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:110-111: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:112: Lost braces 112 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) report_orthologs.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:125: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:126: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:127-128: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:135-137: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:138-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:140-141: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:180-183: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:184-187: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:188-191: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) report_orthologs.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) set_gprofiler.Rd:18: 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 'run_benchmark.Rd': ‘benchmark_homologene’ ‘benchmark_gprofiler’ ‘benchmark_babelgene’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_orthotree 93.101 3.516 112.593 prepare_tree 33.284 0.597 38.107 all_genes 5.315 0.453 23.679 aggregate_mapped_genes 2.911 0.151 10.761 convert_orthologs 1.588 0.075 5.578 map_orthologs 1.155 0.086 5.177 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/orthogene.Rcheck/00check.log’ for details.