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### Running command:
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###   /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
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* 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
GeneTonic                8.986  0.247  14.898
summarize_ggs_hubgenes   8.016  0.281  12.587
ggs_backbone             7.533  0.268  11.709
ggs_graph                7.452  0.236  11.318
gs_mds                   7.391  0.197  11.497
gs_heatmap               7.336  0.188  11.282
gs_upset                 6.590  0.171  10.116
gs_alluvial              6.192  0.189   8.915
enhance_table            6.028  0.178   9.606
gs_dendro                5.701  0.156   9.172
signature_volcano        5.433  0.192   8.591
gs_volcano               5.367  0.152   8.624
gs_horizon               5.367  0.130   7.553
gs_scoresheat            5.065  0.186   7.797
gs_scores                5.025  0.162   7.913
gs_summary_overview_pair 5.003  0.143   7.707
gs_radar                 4.928  0.210   7.656
distill_enrichment       4.973  0.149   7.641
export_for_iSEE          4.971  0.118   7.078
get_aggrscores           4.771  0.135   7.543
enrichment_map           4.707  0.124   6.071
GeneTonicList            4.595  0.136   7.265
checkup_gtl              4.560  0.126   6.922
checkup_GeneTonic        4.498  0.134   6.816
gene_plot                3.898  0.133   5.516
gs_summary_overview      3.757  0.129   5.641
create_kappa_matrix      3.719  0.142   5.867
get_expression_values    3.727  0.116   5.763
gs_summary_heat          3.693  0.139   6.018
* 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