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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_2.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GeneTonic.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.4.2’
* 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 R 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 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   7.405  0.255  10.694
gs_mds                   7.409  0.166  10.874
ggs_backbone             7.057  0.235  10.151
gs_upset                 6.794  0.166  10.361
GeneTonic                6.513  0.228  10.363
ggs_graph                6.203  0.198   9.461
gs_heatmap               6.099  0.182   8.308
gs_scoresheat            5.680  0.159   8.817
signature_volcano        5.427  0.194   8.581
enhance_table            5.331  0.169   7.955
gs_dendro                5.300  0.142   8.143
gs_scores                5.181  0.160   6.739
gs_radar                 4.993  0.230   7.003
gs_volcano               4.774  0.136   7.070
gene_plot                4.562  0.132   7.128
export_for_iSEE          4.522  0.134   6.464
distill_enrichment       4.343  0.136   6.524
gs_summary_overview_pair 4.346  0.133   6.423
gs_alluvial              4.181  0.184   6.303
gs_horizon               4.148  0.132   6.452
enrichment_map           4.045  0.128   5.991
get_aggrscores           4.028  0.125   6.263
GeneTonicList            3.980  0.137   5.803
checkup_GeneTonic        3.929  0.143   5.001
gs_summary_overview      3.877  0.135   5.101
gs_summary_heat          3.623  0.126   5.258
create_kappa_matrix      3.377  0.082   5.229
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK