############################################################################## ############################################################################## ### ### 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 4.4.0 (2024-04-24) * 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 ‘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 12.818 0.403 15.427 summarize_ggs_hubgenes 12.868 0.349 15.356 ggs_backbone 12.756 0.394 16.148 gs_upset 12.827 0.261 15.526 gs_heatmap 12.468 0.299 14.683 ggs_graph 12.221 0.283 14.467 GeneTonic 10.419 0.462 12.550 signature_volcano 9.084 0.320 11.235 gs_dendro 9.079 0.278 10.886 enhance_table 8.954 0.239 10.595 gs_scoresheat 8.530 0.275 11.156 gs_scores 8.491 0.227 10.579 gs_alluvial 7.748 0.382 9.559 gs_horizon 7.905 0.221 9.550 export_for_iSEE 7.542 0.196 9.050 gs_volcano 7.508 0.205 9.499 distill_enrichment 7.186 0.214 8.435 gene_plot 7.074 0.210 8.947 gs_radar 6.703 0.461 8.781 gs_summary_overview_pair 6.878 0.195 8.207 create_kappa_matrix 6.656 0.372 8.221 enrichment_map 6.635 0.204 7.878 checkup_gtl 6.532 0.184 8.140 GeneTonicList 6.405 0.258 7.827 get_aggrscores 6.430 0.218 7.746 checkup_GeneTonic 6.319 0.214 7.637 gs_summary_overview 6.229 0.193 7.719 gs_summary_heat 5.873 0.181 7.311 happy_hour 5.439 0.162 7.065 get_expression_values 4.848 0.181 5.968 * 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