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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneTonic.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings GeneTonic_3.3.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/GeneTonic.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneTonic/DESCRIPTION' ... OK
* this is package 'GeneTonic' version '3.3.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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                 9.76   1.11   10.86
gs_upset               9.00   0.46    9.46
gs_heatmap             7.25   1.27    7.34
ggs_backbone           8.01   0.42    9.45
GeneTonic              7.82   0.35    8.39
signature_volcano      7.76   0.36    8.14
summarize_ggs_hubgenes 7.12   0.40    7.55
ggs_graph              6.39   0.36    6.74
gs_scoresheat          6.40   0.35    6.73
gs_dendro              6.06   0.61    6.64
enhance_table          6.14   0.37    6.51
gs_horizon             5.78   0.23    6.02
gs_scores              5.31   0.47    5.76
gs_summary_overview    5.32   0.16    5.48
create_kappa_matrix    4.66   0.50    5.15
export_for_iSEE        4.89   0.20    5.10
GeneTonicList          4.75   0.28    5.03
gs_alluvial            3.91   0.29    7.07
* 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