############################################################################## ############################################################################## ### ### 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_3.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘3.0.0’ * 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 13.392 0.664 14.196 gs_upset 13.685 0.241 14.597 summarize_ggs_hubgenes 12.719 0.306 13.225 ggs_backbone 12.023 0.300 12.622 gs_heatmap 10.707 0.216 11.757 ggs_graph 10.574 0.248 11.172 enhance_table 9.992 0.203 11.013 gs_scoresheat 9.293 0.245 9.747 gs_dendro 9.033 0.237 9.378 GeneTonic 8.734 0.398 9.734 signature_volcano 8.733 0.284 9.347 gs_scores 8.230 0.203 8.991 gs_volcano 7.477 0.148 7.828 distill_enrichment 7.355 0.174 8.426 gs_summary_overview 7.331 0.190 7.733 export_for_iSEE 7.176 0.130 7.339 gs_alluvial 6.679 0.323 7.147 gene_plot 6.666 0.168 6.905 gs_horizon 6.636 0.170 6.929 create_kappa_matrix 6.350 0.341 7.549 GeneTonicList 6.428 0.197 6.686 checkup_GeneTonic 6.408 0.204 6.790 get_aggrscores 6.459 0.151 6.692 enrichment_map 6.400 0.151 6.789 checkup_gtl 6.276 0.161 6.725 gs_summary_overview_pair 5.824 0.168 6.405 gs_radar 5.646 0.344 6.589 gs_summary_heat 5.668 0.157 5.906 happy_hour 5.226 0.165 5.562 get_expression_values 4.924 0.134 5.507 * 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