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This page was generated on 2025-08-14 11:45 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
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: 2025-08-11 13:40 -0400 (Mon, 11 Aug 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
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 merida1

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: /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_1.22.0.tar.gz
StartedAt: 2025-08-12 08:36:25 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 09:05:51 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 1765.7 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.22.0’
* 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 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-SingleCellExperiment-method 63.104  1.829 110.739
analyse_sc_clusters-Seurat-method               61.035  2.591 118.412
plot_gsva_heatmap-ReactomeAnalysisResult-method 50.145  1.895  94.831
analyse_sc_clusters                             47.760  1.977  84.427
plot_gsva_pca                                   45.451  1.839  84.495
plot_gsva_heatmap                               43.530  1.698  82.621
plot_gsva_pathway                               40.110  1.481  81.506
plot_gsva_pathway-ReactomeAnalysisResult-method 39.252  1.746  80.816
plot_gsva_pca-ReactomeAnalysisResult-method     38.834  1.398  77.060
generate_pseudo_bulk_data                       18.935  1.850 330.978
ReactomeAnalysisRequest                          9.645  0.577  11.405
perform_reactome_analysis                        2.852  0.265  17.959
load_public_dataset                              1.033  0.075   9.370
* 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-3.21-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 ‘1.22.0’
** 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 RC (2025-06-05 r88288) -- "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 
  3.331   0.269   3.930 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest 9.645 0.57711.405
ReactomeAnalysisResult-class0.3270.0200.576
add_dataset-ReactomeAnalysisRequest-DGEList-method1.3120.0711.445
add_dataset-ReactomeAnalysisRequest-EList-method1.3540.0611.428
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method1.2980.0591.381
add_dataset-ReactomeAnalysisRequest-data.frame-method1.2840.0541.357
add_dataset-ReactomeAnalysisRequest-matrix-method1.2800.0521.343
add_dataset1.2840.0421.339
analyse_sc_clusters-Seurat-method 61.035 2.591118.412
analyse_sc_clusters-SingleCellExperiment-method 63.104 1.829110.739
analyse_sc_clusters47.760 1.97784.427
find_public_datasets0.1370.0212.509
generate_metadata0.0020.0000.003
generate_pseudo_bulk_data 18.935 1.850330.978
get_public_species0.0470.0060.510
get_reactome_data_types0.0970.0110.607
get_reactome_methods1.4780.0972.908
get_result-ReactomeAnalysisResult-method0.2390.0160.781
get_result0.2720.0180.291
load_public_dataset1.0330.0759.370
names-ReactomeAnalysisResult-method0.2290.0150.247
open_reactome-ReactomeAnalysisResult-method0.2310.0160.248
open_reactome0.2020.0150.221
pathways-ReactomeAnalysisResult-method0.2840.0160.301
pathways0.1930.0120.205
perform_reactome_analysis 2.852 0.26517.959
plot_correlations-ReactomeAnalysisResult-method0.3180.0180.339
plot_correlations0.2490.0140.265
plot_gsva_heatmap-ReactomeAnalysisResult-method50.145 1.89594.831
plot_gsva_heatmap43.530 1.69882.621
plot_gsva_pathway-ReactomeAnalysisResult-method39.252 1.74680.816
plot_gsva_pathway40.110 1.48181.506
plot_gsva_pca-ReactomeAnalysisResult-method38.834 1.39877.060
plot_gsva_pca45.451 1.83984.495
plot_heatmap-ReactomeAnalysisResult-method0.6090.0231.567
plot_heatmap0.7950.0171.371
plot_volcano-ReactomeAnalysisResult-method0.2330.0150.250
plot_volcano0.3130.0160.331
print-ReactomeAnalysisRequest-method0.0020.0020.003
print-ReactomeAnalysisResult-method0.2730.0200.295
reactome_links-ReactomeAnalysisResult-method0.2280.0160.245
reactome_links0.3210.0210.356
result_types-ReactomeAnalysisResult-method0.3290.0220.370
result_types0.3330.0220.372
set_method-ReactomeAnalysisRequest-method0.0030.0040.008
set_method0.0030.0040.007
set_parameters-ReactomeAnalysisRequest-method0.0030.0010.004
set_parameters0.0030.0000.005
show-ReactomeAnalysisRequest-method0.0020.0020.004
show-ReactomeAnalysisResult-method0.3240.0210.357