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This page was generated on 2025-10-09 12:04 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1727/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 Oct 2025)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: devel
git_last_commit: d9a274e
git_last_commit_date: 2025-04-15 11:49:59 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReactomeGSA on nebbiolo2

To the developers/maintainers of the ReactomeGSA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeGSA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ReactomeGSA
Version: 1.23.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReactomeGSA_1.23.0.tar.gz
StartedAt: 2025-10-09 03:50:19 -0400 (Thu, 09 Oct 2025)
EndedAt: 2025-10-09 04:15:11 -0400 (Thu, 09 Oct 2025)
EllapsedTime: 1491.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ReactomeGSA.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReactomeGSA_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.23.0’
* 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_pathway,ReactomeAnalysisResult-method
> ### Title: ReactomeAnalysisResult - plot_gsva_pathway
> ### Aliases: plot_gsva_pathway,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

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
> 
> # create the plot
> plot_obj <- plot_gsva_pathway(gsva_result, "R-HSA-389542")
Error: C stack usage  7969732 is too close to the limit
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
plot_gsva_heatmap-ReactomeAnalysisResult-method 46.066  1.740 195.386
analyse_sc_clusters                             43.776  1.735 207.202
analyse_sc_clusters-Seurat-method               36.954  2.242 115.177
plot_gsva_heatmap                               36.964  1.002 105.733
analyse_sc_clusters-SingleCellExperiment-method 35.868  1.475 113.505
generate_pseudo_bulk_data                       14.027  1.132  15.177
ReactomeAnalysisRequest                          4.854  0.226   5.082
load_public_dataset                              3.597  0.226  29.118
perform_reactome_analysis                        3.434  0.238  29.192
find_public_datasets                             0.487  0.036   5.766
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown

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--- finished re-building ‘analysing-scRNAseq.Rmd’

--- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown
--- finished re-building ‘reanalysing-public-data.Rmd’

--- re-building ‘using-reactomegsa.Rmd’ using rmarkdown

Quitting from using-reactomegsa.Rmd:219-221 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'result_types' for signature 'x = "NULL"'
---
Backtrace:
    ▆
 1. └─ReactomeGSA::result_types(result)
 2.   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'using-reactomegsa.Rmd' failed with diagnostics:
unable to find an inherited method for function 'result_types' for signature 'x = "NULL"'
--- failed re-building ‘using-reactomegsa.Rmd’

SUMMARY: processing the following file failed:
  ‘using-reactomegsa.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ReactomeGSA’ ...
** this is package ‘ReactomeGSA’ version ‘1.23.0’
** 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)

Tests output

ReactomeGSA.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  1.685   0.134   1.807 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest4.8540.2265.082
ReactomeAnalysisResult-class0.1790.0070.187
add_dataset-ReactomeAnalysisRequest-DGEList-method0.8620.0140.878
add_dataset-ReactomeAnalysisRequest-EList-method0.5100.0050.515
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.5030.0170.520
add_dataset-ReactomeAnalysisRequest-data.frame-method0.5080.0060.514
add_dataset-ReactomeAnalysisRequest-matrix-method0.5070.0020.509
add_dataset0.5100.0010.511
analyse_sc_clusters-Seurat-method 36.954 2.242115.177
analyse_sc_clusters-SingleCellExperiment-method 35.868 1.475113.505
analyse_sc_clusters 43.776 1.735207.202
find_public_datasets0.4870.0365.766
generate_metadata0.0010.0010.003
generate_pseudo_bulk_data14.027 1.13215.177
get_public_species0.1620.0350.698
get_reactome_data_types0.3820.0151.394
get_reactome_methods0.5670.0392.308
get_result-ReactomeAnalysisResult-method0.5650.0610.625
get_result0.2190.0060.225
load_public_dataset 3.597 0.22629.118
names-ReactomeAnalysisResult-method0.2100.0050.215
open_reactome-ReactomeAnalysisResult-method0.2010.0110.212
open_reactome0.1940.0060.200
pathways-ReactomeAnalysisResult-method0.2480.0070.255
pathways0.2140.0070.222
perform_reactome_analysis 3.434 0.23829.192
plot_correlations-ReactomeAnalysisResult-method0.3200.0160.337
plot_correlations0.2630.0040.266
plot_gsva_heatmap-ReactomeAnalysisResult-method 46.066 1.740195.386
plot_gsva_heatmap 36.964 1.002105.733