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This page was generated on 2025-08-23 12:04 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1711/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 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 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: 2025-08-23 01:52:59 -0400 (Sat, 23 Aug 2025)
EndedAt: 2025-08-23 02:10:13 -0400 (Sat, 23 Aug 2025)
EllapsedTime: 1034.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

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
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
plot_gsva_heatmap-ReactomeAnalysisResult-method 33.422  2.073  67.081
plot_gsva_pathway                               32.924  1.673  66.746
plot_gsva_pca-ReactomeAnalysisResult-method     32.731  1.745  67.403
plot_gsva_heatmap                               32.687  1.781  67.467
plot_gsva_pca                                   32.625  1.710  66.750
analyse_sc_clusters-Seurat-method               32.782  1.416  75.769
plot_gsva_pathway-ReactomeAnalysisResult-method 31.833  1.796  65.183
analyse_sc_clusters                             31.144  1.271  67.035
analyse_sc_clusters-SingleCellExperiment-method 30.463  1.021  65.068
generate_pseudo_bulk_data                       15.059  1.450  16.554
perform_reactome_analysis                        4.424  0.622  16.644
load_public_dataset                              3.863  0.471  33.510
find_public_datasets                             0.448  0.027   6.437
* 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 ... OK
* 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/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 (2025-06-13) -- "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 
  1.602   0.185   1.654 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest4.6470.2134.862
ReactomeAnalysisResult-class0.1940.0050.199
add_dataset-ReactomeAnalysisRequest-DGEList-method0.9060.0400.946
add_dataset-ReactomeAnalysisRequest-EList-method0.5410.0040.545
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.5240.0050.529
add_dataset-ReactomeAnalysisRequest-data.frame-method0.5280.0040.532
add_dataset-ReactomeAnalysisRequest-matrix-method0.5600.0020.562
add_dataset0.5440.0070.551
analyse_sc_clusters-Seurat-method32.782 1.41675.769
analyse_sc_clusters-SingleCellExperiment-method30.463 1.02165.068
analyse_sc_clusters31.144 1.27167.035
find_public_datasets0.4480.0276.437
generate_metadata0.0010.0020.004
generate_pseudo_bulk_data15.059 1.45016.554
get_public_species0.1410.0050.592
get_reactome_data_types0.2600.0291.989
get_reactome_methods0.3090.0132.075
get_result-ReactomeAnalysisResult-method0.2440.0200.265
get_result0.2300.0140.244
load_public_dataset 3.863 0.47133.510
names-ReactomeAnalysisResult-method0.2270.0310.258
open_reactome-ReactomeAnalysisResult-method0.2110.0130.225
open_reactome0.2120.0140.226
pathways-ReactomeAnalysisResult-method0.2590.0240.284
pathways0.2220.0200.242
perform_reactome_analysis 4.424 0.62216.644
plot_correlations-ReactomeAnalysisResult-method0.2600.0380.298
plot_correlations0.2320.0100.242
plot_gsva_heatmap-ReactomeAnalysisResult-method33.422 2.07367.081
plot_gsva_heatmap32.687 1.78167.467
plot_gsva_pathway-ReactomeAnalysisResult-method31.833 1.79665.183
plot_gsva_pathway32.924 1.67366.746
plot_gsva_pca-ReactomeAnalysisResult-method32.731 1.74567.403
plot_gsva_pca32.625 1.71066.750
plot_heatmap-ReactomeAnalysisResult-method0.4260.0290.455
plot_heatmap0.5330.0420.576
plot_volcano-ReactomeAnalysisResult-method0.1910.0100.201
plot_volcano0.2200.0100.229
print-ReactomeAnalysisRequest-method0.0010.0000.002
print-ReactomeAnalysisResult-method0.1990.0040.203
reactome_links-ReactomeAnalysisResult-method0.1940.0020.196
reactome_links0.1950.0030.199
result_types-ReactomeAnalysisResult-method0.1920.0050.196
result_types0.2040.0080.213
set_method-ReactomeAnalysisRequest-method0.0020.0000.002
set_method0.0010.0000.002
set_parameters-ReactomeAnalysisRequest-method0.0010.0000.001
set_parameters0.0020.0000.001
show-ReactomeAnalysisRequest-method0.0010.0000.001
show-ReactomeAnalysisResult-method0.2100.0190.230