############################################################################## ############################################################################## ### ### 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_2.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.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 ‘GeneTonic/DESCRIPTION’ ... OK * this is package ‘GeneTonic’ version ‘2.9.0’ * 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 summarize_ggs_hubgenes 12.865 0.319 15.342 gs_mds 12.836 0.318 14.449 gs_upset 12.761 0.267 15.525 ggs_backbone 12.645 0.305 14.147 gs_heatmap 12.369 0.248 14.543 ggs_graph 12.188 0.246 13.752 GeneTonic 10.211 0.426 11.538 gs_dendro 9.170 0.227 10.499 signature_volcano 9.000 0.272 10.144 enhance_table 8.906 0.201 9.806 gs_scores 8.777 0.173 9.616 gs_scoresheat 8.435 0.305 9.678 gs_horizon 7.896 0.219 9.034 gs_alluvial 7.742 0.321 8.877 export_for_iSEE 7.579 0.192 8.810 gs_volcano 7.429 0.198 8.587 distill_enrichment 7.323 0.220 8.367 gs_radar 6.880 0.354 8.037 gene_plot 6.991 0.187 7.942 create_kappa_matrix 6.648 0.333 7.802 gs_summary_overview_pair 6.774 0.207 8.239 enrichment_map 6.673 0.179 8.133 GeneTonicList 6.522 0.211 7.274 get_aggrscores 6.496 0.193 7.294 checkup_gtl 6.432 0.158 7.114 checkup_GeneTonic 6.374 0.196 6.969 gs_summary_overview 6.150 0.179 6.938 gs_summary_heat 5.860 0.150 6.827 happy_hour 5.283 0.147 5.700 get_expression_values 4.850 0.160 5.470 * 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