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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/meat/GeneTonic.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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
gs_mds                   13.122  0.526  16.601
gs_upset                 12.708  0.255  16.735
ggs_backbone             11.732  0.342  15.324
summarize_ggs_hubgenes   11.495  0.303  15.649
gs_heatmap               10.732  0.308  13.961
ggs_graph                10.471  0.293  14.470
signature_volcano         9.525  0.326  14.013
gs_scoresheat             9.169  0.463  13.021
GeneTonic                 8.914  0.421  11.935
gs_dendro                 8.870  0.245  11.670
gs_scores                 8.465  0.405  11.957
distill_enrichment        7.782  0.255  10.299
gs_horizon                7.727  0.276   9.725
enhance_table             7.604  0.172   9.844
gene_plot                 7.257  0.186   9.351
gs_summary_overview       6.995  0.297   9.597
export_for_iSEE           7.103  0.160   9.182
gs_radar                  6.785  0.469   9.672
gs_alluvial               6.475  0.326   9.095
gs_volcano                6.439  0.190   8.637
create_kappa_matrix       6.202  0.425   8.437
enrichment_map            6.288  0.162   8.129
GeneTonicList             6.229  0.212   8.226
checkup_gtl               6.171  0.182   7.933
checkup_GeneTonic         6.162  0.176   7.682
get_aggrscores            5.999  0.192   8.167
gs_summary_overview_pair  5.861  0.217   8.895
gs_summary_heat           5.778  0.216   7.939
happy_hour                5.361  0.177   7.836
get_expression_values     3.872  0.170   5.098
* 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