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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_3.0.0.tar.gz
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* 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                   13.343  0.422  14.968
summarize_ggs_hubgenes   12.768  0.300  13.996
gs_upset                 12.408  0.220  13.586
ggs_graph                11.625  0.270  12.065
ggs_backbone             11.123  0.347  11.961
gs_heatmap               10.781  0.246  11.830
gs_scores                10.687  0.301  12.144
signature_volcano         9.896  0.341  10.934
gs_dendro                 9.149  0.296  10.593
GeneTonic                 8.902  0.440  10.014
enhance_table             9.036  0.241  10.119
gs_scoresheat             8.277  0.273   8.983
gs_horizon                7.660  0.171   8.361
gs_volcano                7.583  0.233   8.880
gs_summary_overview       7.254  0.267   8.580
distill_enrichment        7.245  0.186   8.525
gs_summary_overview_pair  6.977  0.219   7.878
gs_alluvial               6.745  0.342  10.116
gene_plot                 6.654  0.186   7.343
GeneTonicList             6.521  0.240   6.948
enrichment_map            6.509  0.203   7.037
create_kappa_matrix       6.339  0.344   7.643
get_aggrscores            6.456  0.210   6.765
checkup_GeneTonic         6.313  0.157   6.611
checkup_gtl               6.255  0.184   6.542
export_for_iSEE           6.249  0.169   6.748
gs_radar                  5.767  0.339   6.982
gs_summary_heat           5.733  0.209   6.519
happy_hour                5.402  0.210   6.187
get_expression_values     4.879  0.136   5.180
* 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