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This page was generated on 2025-09-27 12:05 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1722/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 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    OK  UNNEEDED, same version is already published
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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReactomeGSA_1.23.0.tar.gz
StartedAt: 2025-09-26 23:35:12 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 23:51:51 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 998.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReactomeGSA_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.23.0’
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
analyse_sc_clusters-Seurat-method               36.646  1.580  80.422
plot_gsva_pca-ReactomeAnalysisResult-method     35.966  1.602  73.656
plot_gsva_heatmap                               35.840  1.505  93.099
plot_gsva_pathway                               35.673  1.627 117.005
plot_gsva_heatmap-ReactomeAnalysisResult-method 35.604  1.493  76.336
plot_gsva_pca                                   35.043  1.536  79.390
plot_gsva_pathway-ReactomeAnalysisResult-method 34.390  1.563  77.387
analyse_sc_clusters-SingleCellExperiment-method 34.080  1.394  75.281
analyse_sc_clusters                             33.661  1.489  77.086
generate_pseudo_bulk_data                       14.700  1.893  16.775
ReactomeAnalysisRequest                          6.004  0.370   6.427
perform_reactome_analysis                        3.642  0.313  79.306
load_public_dataset                              1.945  0.173  43.064
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  2.170   0.221   2.404 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.0040.3706.427
ReactomeAnalysisResult-class0.2350.0160.255
add_dataset-ReactomeAnalysisRequest-DGEList-method1.1020.0541.162
add_dataset-ReactomeAnalysisRequest-EList-method0.7410.0420.789
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.7040.0530.761
add_dataset-ReactomeAnalysisRequest-data.frame-method0.7680.0410.816
add_dataset-ReactomeAnalysisRequest-matrix-method0.7550.0390.802
add_dataset0.7160.0410.761
analyse_sc_clusters-Seurat-method36.646 1.58080.422
analyse_sc_clusters-SingleCellExperiment-method34.080 1.39475.281
analyse_sc_clusters33.661 1.48977.086
find_public_datasets0.1110.0142.932
generate_metadata0.0010.0000.002
generate_pseudo_bulk_data14.700 1.89316.775
get_public_species0.0260.0030.316
get_reactome_data_types0.0510.0080.745
get_reactome_methods0.0910.0120.982
get_result-ReactomeAnalysisResult-method0.4960.0770.578
get_result0.2180.0100.231
load_public_dataset 1.945 0.17343.064
names-ReactomeAnalysisResult-method0.2530.0130.271
open_reactome-ReactomeAnalysisResult-method0.2520.0130.271
open_reactome0.2510.0130.267
pathways-ReactomeAnalysisResult-method0.3260.0140.343
pathways0.2760.0150.297
perform_reactome_analysis 3.642 0.31379.306
plot_correlations-ReactomeAnalysisResult-method0.3330.0100.345
plot_correlations0.3100.0110.323
plot_gsva_heatmap-ReactomeAnalysisResult-method35.604 1.49376.336
plot_gsva_heatmap35.840 1.50593.099
plot_gsva_pathway-ReactomeAnalysisResult-method34.390 1.56377.387
plot_gsva_pathway 35.673 1.627117.005
plot_gsva_pca-ReactomeAnalysisResult-method35.966 1.60273.656
plot_gsva_pca35.043 1.53679.390
plot_heatmap-ReactomeAnalysisResult-method0.6330.0170.656
plot_heatmap0.8480.0850.941
plot_volcano-ReactomeAnalysisResult-method0.2600.0100.272
plot_volcano0.2780.0110.294
print-ReactomeAnalysisRequest-method0.0010.0000.003
print-ReactomeAnalysisResult-method0.2410.0110.254
reactome_links-ReactomeAnalysisResult-method0.2300.0120.244
reactome_links0.2320.0110.246
result_types-ReactomeAnalysisResult-method0.2360.0100.250
result_types0.2500.0110.262
set_method-ReactomeAnalysisRequest-method0.0020.0030.004
set_method0.0020.0020.004
set_parameters-ReactomeAnalysisRequest-method0.0020.0000.002
set_parameters0.0020.0000.002
show-ReactomeAnalysisRequest-method0.0020.0010.003
show-ReactomeAnalysisResult-method0.2550.0130.271