##############################################################################
##############################################################################
###
### 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_2.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GeneTonic.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.0.2’
* 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 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                   11.933  0.389  12.401
summarize_ggs_hubgenes   11.777  0.232  12.043
gs_upset                 11.044  0.210  11.290
ggs_backbone             10.999  0.210  11.242
gs_heatmap               10.634  0.191  10.843
ggs_graph                10.477  0.184  10.693
GeneTonic                 9.346  0.338   9.701
gs_scoresheat             8.671  0.191   8.894
gs_scores                 8.601  0.191   8.822
gs_dendro                 8.140  0.227   8.382
signature_volcano         8.111  0.190   8.324
gs_horizon                7.482  0.133   7.687
gene_plot                 6.866  0.165   7.050
export_for_iSEE           6.887  0.109   7.004
gs_summary_overview       6.526  0.140   6.682
gs_radar                  6.424  0.216   6.661
distill_enrichment        6.426  0.137   6.577
GeneTonicList             6.040  0.163   6.214
checkup_gtl               5.960  0.165   6.144
enrichment_map            5.979  0.142   6.133
checkup_GeneTonic         5.942  0.153   6.108
gs_volcano                5.951  0.132   6.111
create_kappa_matrix       5.663  0.377   6.050
happy_hour                5.792  0.134   5.938
get_aggrscores            5.788  0.086   5.880
gs_alluvial               5.575  0.190   5.783
gs_summary_heat           5.429  0.140   5.575
gs_summary_overview_pair  5.394  0.133   5.587
enhance_table             5.341  0.107   5.456
* 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