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This page was generated on 2025-08-04 11:41 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1728/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.22.0  (landing page)
Johannes Griss
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_21
git_last_commit: 6e8adbb
git_last_commit_date: 2025-04-15 11:49:59 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReactomeGSA on nebbiolo1

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: 1.22.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeGSA_1.22.0.tar.gz
StartedAt: 2025-08-04 01:52:01 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 02:09:41 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 1059.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeGSA_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.2 LTS
* using session charset: UTF-8
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
plot_gsva_heatmap-ReactomeAnalysisResult-method 34.534  2.304  73.009
plot_gsva_pca-ReactomeAnalysisResult-method     32.910  1.877  69.920
plot_gsva_heatmap                               32.970  1.693  68.406
plot_gsva_pca                                   32.568  1.896  65.935
plot_gsva_pathway-ReactomeAnalysisResult-method 32.655  1.727  68.662
plot_gsva_pathway                               32.095  1.641  65.100
analyse_sc_clusters                             31.962  1.573  68.130
analyse_sc_clusters-Seurat-method               32.080  1.419  70.222
analyse_sc_clusters-SingleCellExperiment-method 31.520  1.825  74.118
generate_pseudo_bulk_data                       15.081  2.214  17.349
load_public_dataset                              4.809  0.485  40.846
perform_reactome_analysis                        4.440  0.729  19.051
ReactomeAnalysisRequest                          4.744  0.258   5.003
* 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-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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)

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 
  1.699   0.090   1.776 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest4.7440.2585.003
ReactomeAnalysisResult-class0.1880.0050.194
add_dataset-ReactomeAnalysisRequest-DGEList-method0.8230.0280.851
add_dataset-ReactomeAnalysisRequest-EList-method0.5280.0050.533
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.5210.0020.525
add_dataset-ReactomeAnalysisRequest-data.frame-method0.5030.0030.506
add_dataset-ReactomeAnalysisRequest-matrix-method0.5160.0010.519
add_dataset0.5110.0030.514
analyse_sc_clusters-Seurat-method32.080 1.41970.222
analyse_sc_clusters-SingleCellExperiment-method31.520 1.82574.118
analyse_sc_clusters31.962 1.57368.130
find_public_datasets0.5330.0213.531
generate_metadata0.0010.0050.005
generate_pseudo_bulk_data15.081 2.21417.349
get_public_species0.1430.0030.588
get_reactome_data_types0.3600.0331.270
get_reactome_methods0.5380.0541.926
get_result-ReactomeAnalysisResult-method0.2450.0530.298
get_result0.2240.0160.240
load_public_dataset 4.809 0.48540.846
names-ReactomeAnalysisResult-method0.2170.0200.237
open_reactome-ReactomeAnalysisResult-method0.1980.0240.223
open_reactome0.1910.0070.198
pathways-ReactomeAnalysisResult-method0.2380.0270.266
pathways0.2070.0090.216
perform_reactome_analysis 4.440 0.72919.051
plot_correlations-ReactomeAnalysisResult-method0.3060.0320.338
plot_correlations0.2990.0210.321
plot_gsva_heatmap-ReactomeAnalysisResult-method34.534 2.30473.009
plot_gsva_heatmap32.970 1.69368.406
plot_gsva_pathway-ReactomeAnalysisResult-method32.655 1.72768.662
plot_gsva_pathway32.095 1.64165.100
plot_gsva_pca-ReactomeAnalysisResult-method32.910 1.87769.920
plot_gsva_pca32.568 1.89665.935
plot_heatmap-ReactomeAnalysisResult-method0.4300.0390.469
plot_heatmap0.5500.0490.599
plot_volcano-ReactomeAnalysisResult-method0.2130.0140.227
plot_volcano0.2300.0110.241
print-ReactomeAnalysisRequest-method0.0020.0000.001
print-ReactomeAnalysisResult-method0.2210.0030.224
reactome_links-ReactomeAnalysisResult-method0.2090.0160.224
reactome_links0.2060.0040.209
result_types-ReactomeAnalysisResult-method0.2140.0040.218
result_types0.2120.0100.221
set_method-ReactomeAnalysisRequest-method0.0020.0000.002
set_method0.0010.0010.002
set_parameters-ReactomeAnalysisRequest-method0.0010.0010.002
set_parameters0.0010.0000.002
show-ReactomeAnalysisRequest-method0.0000.0010.002
show-ReactomeAnalysisResult-method0.2220.0060.228