############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneTonic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneTonic_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneTonic/DESCRIPTION’ ... OK * this is package ‘GeneTonic’ version ‘2.8.0’ * 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 ‘GeneTonic’ 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed gs_mds 12.945 0.479 15.244 gs_upset 12.600 0.265 15.266 summarize_ggs_hubgenes 11.706 0.318 14.091 ggs_graph 11.682 0.281 13.847 ggs_backbone 11.498 0.321 13.672 gs_heatmap 10.808 0.415 12.513 signature_volcano 9.728 0.349 12.144 GeneTonic 9.340 0.451 11.235 gs_scoresheat 9.191 0.293 12.336 gs_dendro 8.839 0.222 10.278 gs_scores 8.315 0.264 10.257 enhance_table 7.739 0.200 8.741 gene_plot 7.674 0.226 8.997 gs_horizon 7.626 0.233 9.067 GeneTonicList 7.084 0.250 8.110 gs_summary_overview 6.990 0.247 8.490 distill_enrichment 6.822 0.186 7.843 gs_radar 6.528 0.399 7.847 create_kappa_matrix 6.276 0.480 7.815 gs_volcano 6.548 0.173 8.286 gs_alluvial 6.379 0.316 7.553 export_for_iSEE 6.469 0.154 7.657 enrichment_map 6.344 0.181 7.147 happy_hour 6.324 0.200 8.468 checkup_GeneTonic 6.202 0.203 7.162 checkup_gtl 6.130 0.237 7.480 get_aggrscores 6.184 0.162 7.221 gs_summary_overview_pair 5.819 0.187 7.089 gs_summary_heat 5.706 0.174 7.175 get_expression_values 4.762 0.179 5.678 * 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: OK