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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_2.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneTonic.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneTonic/DESCRIPTION’ ... OK
* this is package ‘GeneTonic’ version ‘2.9.0’
* 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                8.792  0.238   9.151
ggs_backbone             7.649  0.302   8.133
summarize_ggs_hubgenes   7.595  0.336   7.997
gs_mds                   7.547  0.383   8.091
ggs_graph                7.058  0.257   7.453
gs_upset                 6.957  0.202   7.189
gs_heatmap               6.823  0.219   7.151
gs_alluvial              6.359  0.247   6.636
signature_volcano        6.222  0.259   6.540
enhance_table            6.128  0.212   6.381
gs_dendro                6.098  0.221   6.342
gs_horizon               5.631  0.194   5.903
gs_scoresheat            5.463  0.290   5.893
gs_radar                 5.331  0.243   5.648
distill_enrichment       5.358  0.213   5.602
gs_summary_overview_pair 5.334  0.174   5.567
export_for_iSEE          5.320  0.178   5.530
enrichment_map           5.132  0.193   5.380
gs_scores                5.033  0.256   5.376
gs_volcano               5.063  0.178   5.294
checkup_GeneTonic        5.036  0.202   5.312
checkup_gtl              5.026  0.195   5.329
get_aggrscores           5.006  0.174   5.217
GeneTonicList            4.917  0.166   5.128
* 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