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This page was generated on 2025-08-20 12:07 -0400 (Wed, 20 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 1709/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 Aug 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ReactomeGSA
Version: 1.23.0
Command: /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_1.23.0.tar.gz
StartedAt: 2025-08-19 11:29:14 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 11:46:57 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 1063.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
plot_gsva_pathway                               57.174  0.495  97.749
plot_gsva_heatmap                               56.317  0.597  99.194
plot_gsva_heatmap-ReactomeAnalysisResult-method 55.738  0.575 107.904
plot_gsva_pathway-ReactomeAnalysisResult-method 55.068  0.537 100.478
plot_gsva_pca                                   54.856  0.510 106.654
plot_gsva_pca-ReactomeAnalysisResult-method     53.449  0.595  98.544
analyse_sc_clusters                             50.126  0.576  99.202
analyse_sc_clusters-Seurat-method               47.819  1.743  95.442
analyse_sc_clusters-SingleCellExperiment-method 48.515  1.003  94.262
generate_pseudo_bulk_data                       18.550  0.622  19.340
ReactomeAnalysisRequest                          6.731  0.607   7.367
perform_reactome_analysis                        4.886  0.075  26.146
load_public_dataset                              1.214  0.016  10.981
find_public_datasets                             0.146  0.015   6.515
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 
  2.116   0.216   2.326 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.7310.6077.367
ReactomeAnalysisResult-class0.2290.0040.236
add_dataset-ReactomeAnalysisRequest-DGEList-method1.1800.1111.295
add_dataset-ReactomeAnalysisRequest-EList-method0.8910.0040.898
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.9050.0080.916
add_dataset-ReactomeAnalysisRequest-data.frame-method0.8760.0160.894
add_dataset-ReactomeAnalysisRequest-matrix-method0.8900.0360.929
add_dataset0.8890.0040.896
analyse_sc_clusters-Seurat-method47.819 1.74395.442
analyse_sc_clusters-SingleCellExperiment-method48.515 1.00394.262
analyse_sc_clusters50.126 0.57699.202
find_public_datasets0.1460.0156.515
generate_metadata0.0010.0000.001
generate_pseudo_bulk_data18.550 0.62219.340
get_public_species0.0420.0081.294
get_reactome_data_types0.0950.0042.200
get_reactome_methods0.1580.0094.745
get_result-ReactomeAnalysisResult-method0.2490.0000.249
get_result0.2470.0000.247
load_public_dataset 1.214 0.01610.981
names-ReactomeAnalysisResult-method0.2460.0000.247
open_reactome-ReactomeAnalysisResult-method0.2530.0000.254
open_reactome0.2500.0040.254
pathways-ReactomeAnalysisResult-method0.3280.0000.330
pathways0.2600.0040.265
perform_reactome_analysis 4.886 0.07526.146
plot_correlations-ReactomeAnalysisResult-method0.3300.0040.336
plot_correlations0.3080.0000.309
plot_gsva_heatmap-ReactomeAnalysisResult-method 55.738 0.575107.904
plot_gsva_heatmap56.317 0.59799.194
plot_gsva_pathway-ReactomeAnalysisResult-method 55.068 0.537100.478
plot_gsva_pathway57.174 0.49597.749
plot_gsva_pca-ReactomeAnalysisResult-method53.449 0.59598.544
plot_gsva_pca 54.856 0.510106.654
plot_heatmap-ReactomeAnalysisResult-method0.5330.0000.534
plot_heatmap0.7080.0120.722
plot_volcano-ReactomeAnalysisResult-method0.2530.0040.258
plot_volcano0.2810.0050.288
print-ReactomeAnalysisRequest-method0.0010.0000.002
print-ReactomeAnalysisResult-method0.2170.0160.234
reactome_links-ReactomeAnalysisResult-method0.2290.0040.234
reactome_links0.2250.0040.230
result_types-ReactomeAnalysisResult-method0.2280.0040.233
result_types0.2210.0080.230
set_method-ReactomeAnalysisRequest-method0.0020.0000.002
set_method0.0020.0000.002
set_parameters-ReactomeAnalysisRequest-method0.0020.0000.002
set_parameters0.0020.0000.002
show-ReactomeAnalysisRequest-method0.0010.0000.002
show-ReactomeAnalysisResult-method0.2320.0040.238