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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReactomeGSA_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.22.0’
* 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 ‘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 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 loading without being on the library search path ... 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 ... 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ReactomeGSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_gsva_heatmap,ReactomeAnalysisResult-method
> ### Title: plot_gsva_heatmap - ReactomeAnalysisResult function
> ### Aliases: plot_gsva_heatmap,ReactomeAnalysisResult-method
> 
> ### ** Examples
> 
> # load the scRNA-seq example data
> library(ReactomeGSA.data)
Loading required package: limma
Loading required package: edgeR
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
'SeuratObject' was built with package 'Matrix' 1.7.2 but the current
version is 1.7.3; it is recomended that you reinstall 'SeuratObject' as
the ABI for 'Matrix' may have changed

Attaching package: 'SeuratObject'

The following objects are masked from 'package:base':

    intersect, t

> data(jerby_b_cells)
> 
> # perform the GSVA analysis
> gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE)
Converting expression data to string... (This may take a moment)
Conversion complete
Compressing request data...
Reactome Analysis submitted succesfully
> 
> # plot the heatmap
> relevant_pathways <- c("R-HSA-983170", "R-HSA-388841", "R-HSA-2132295", 
+                        "R-HSA-983705", "R-HSA-5690714")
> plot_gsva_heatmap(gsva_result, 
+                   pathway_ids = relevant_pathways, # limit to these pathways
+                   margins = c(6,30), # adapt the figure margins in heatmap.2
+                   dendrogram = "col", # only plot column dendrogram
+                   scale = "row", # scale for each pathway
+                   key = FALSE, # don't display the color key
+                   lwid=c(0.1,4)) # remove the white space on the left
Error: C stack usage  7969280 is too close to the limit
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
analyse_sc_clusters                             51.984  1.646 107.168
analyse_sc_clusters-Seurat-method               51.980  1.038  98.645
analyse_sc_clusters-SingleCellExperiment-method 42.762  0.845  87.831
generate_pseudo_bulk_data                       20.813  1.894  22.981
ReactomeAnalysisRequest                          7.093  0.224   7.337
perform_reactome_analysis                        4.318  0.500  65.817
load_public_dataset                              1.937  0.240  39.835
find_public_datasets                             0.162  0.012   6.208
* 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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReactomeGSA
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘ReactomeGSA’ ...
** this is package ‘ReactomeGSA’ version ‘1.22.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘analyse_sc_clusters’ with signature ‘object="Seurat"’: no definition for class “Seurat”
in method for ‘analyse_sc_clusters’ with signature ‘object="SingleCellExperiment"’: no definition for class “SingleCellExperiment”
in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="EList"’: no definition for class “EList”
in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="DGEList"’: no definition for class “DGEList”
in method for ‘generate_pseudo_bulk_data’ with signature ‘object="Seurat"’: no definition for class “Seurat”
in method for ‘generate_pseudo_bulk_data’ with signature ‘object="SingleCellExperiment"’: no definition for class “SingleCellExperiment”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ReactomeGSA)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ReactomeGSA)
> 
> test_check("ReactomeGSA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  2.477   0.157   2.627