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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ReactomeGSA_1.13.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ReactomeGSA.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ReactomeGSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ReactomeGSA' version '1.13.0'
* 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 whether package 'ReactomeGSA' 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 ... NOTE
plot_correlations,ReactomeAnalysisResult: no visible binding for global
  variable 'combined_sig'
plot_correlations,ReactomeAnalysisResult: no visible binding for global
  variable 'alpha'
plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global
  variable 'cluster_id'
plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global
  variable 'expr'
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
  variable 'gsva_result'
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
  variable 'PC1'
plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global
  variable 'PC2'
plot_heatmap,ReactomeAnalysisResult: no visible global function
  definition for 'desc'
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
  variable 'n_sig'
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
  variable 'dataset'
plot_heatmap,ReactomeAnalysisResult: no visible binding for global
  variable 'Name'
plot_volcano,ReactomeAnalysisResult: no visible binding for global
  variable 'av_foldchange'
plot_volcano,ReactomeAnalysisResult: no visible binding for global
  variable 'FDR'
Undefined global functions or variables:
  FDR Name PC1 PC2 alpha av_foldchange cluster_id combined_sig dataset
  desc expr gsva_result n_sig
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plot_heatmap,ReactomeAnalysisResult-method':
\S4method{plot_heatmap}{ReactomeAnalysisResult}
  Code: function(x, fdr = 0.01, max_pathways = 30, break_long_names =
                 TRUE, return_data = FALSE)
  Docs: function(x, fdr = 0.05, max_pathways = 30, break_long_names =
                 TRUE, return_data = FALSE)
  Mismatches in argument default values:
    Name: 'fdr' Code: 0.01 Docs: 0.05

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                 user system elapsed
analyse_sc_clusters-Seurat-method               26.11   1.99   86.87
analyse_sc_clusters                             25.12   1.60   80.51
analyse_sc_clusters-SingleCellExperiment-method 24.75   1.97   85.38
plot_gsva_pathway                               25.39   1.33   83.53
plot_gsva_heatmap                               24.71   1.47   84.18
plot_gsva_pca-ReactomeAnalysisResult-method     24.53   1.34   79.61
plot_gsva_pathway-ReactomeAnalysisResult-method 24.52   1.30   81.47
plot_gsva_pca                                   24.51   1.02   80.40
plot_gsva_heatmap-ReactomeAnalysisResult-method 24.30   1.11   81.86
perform_reactome_analysis                        1.61   0.19   18.40
* 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: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ReactomeGSA.Rcheck/00check.log'
for details.