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This page was generated on 2025-03-31 12:09 -0400 (Mon, 31 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1698/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.20.0  (landing page)
Johannes Griss
Snapshot Date: 2025-03-27 13:00 -0400 (Thu, 27 Mar 2025)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_20
git_last_commit: b1f2efd
git_last_commit_date: 2024-10-29 10:40:10 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    TIMEOUT  
palomino8Windows 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
taishanLinux (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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2025-03-28 08:40:29 -0400 (Fri, 28 Mar 2025)
EndedAt: 2025-03-28 09:02:36 -0400 (Fri, 28 Mar 2025)
EllapsedTime: 1327.0 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_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.20.0’
* 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
plot_gsva_heatmap-ReactomeAnalysisResult-method 79.811  1.611 116.086
analyse_sc_clusters-Seurat-method               78.181  1.874 121.801
plot_gsva_heatmap                               78.131  1.732 115.287
plot_gsva_pca                                   77.874  1.971 147.984
plot_gsva_pathway                               77.791  1.643 113.427
plot_gsva_pathway-ReactomeAnalysisResult-method 77.239  2.108 116.606
analyse_sc_clusters-SingleCellExperiment-method 76.845  1.761 112.363
plot_gsva_pca-ReactomeAnalysisResult-method     76.751  1.685 114.705
analyse_sc_clusters                             75.749  2.095 110.807
ReactomeAnalysisRequest                         11.153  0.700  13.141
perform_reactome_analysis                        5.943  0.421  56.589
load_public_dataset                              2.828  0.216  39.476
* 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-3.20-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ReactomeGSA’ ...
** 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”
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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 
  3.202   0.293   3.463 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest11.153 0.70013.141
ReactomeAnalysisResult-class3.7980.0333.935
add_dataset-ReactomeAnalysisRequest-DGEList-method1.4630.1171.593
add_dataset-ReactomeAnalysisRequest-EList-method1.3550.0701.433
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method1.360.091.46
add_dataset-ReactomeAnalysisRequest-data.frame-method1.6350.0691.714
add_dataset-ReactomeAnalysisRequest-matrix-method1.3120.0881.405
add_dataset1.2930.0591.361
analyse_sc_clusters-Seurat-method 78.181 1.874121.801
analyse_sc_clusters-SingleCellExperiment-method 76.845 1.761112.363
analyse_sc_clusters 75.749 2.095110.807
find_public_datasets0.1900.0244.293
get_public_species0.0470.0060.543
get_reactome_data_types0.0970.0120.782
get_reactome_methods0.1650.0231.224
get_result-ReactomeAnalysisResult-method0.3090.0160.331
get_result0.3000.0160.318
load_public_dataset 2.828 0.21639.476
names-ReactomeAnalysisResult-method0.3400.1000.468
open_reactome-ReactomeAnalysisResult-method0.2990.0150.336
open_reactome0.3000.0180.382
pathways-ReactomeAnalysisResult-method4.0190.0404.114
pathways3.8410.0243.879
perform_reactome_analysis 5.943 0.42156.589
plot_correlations-ReactomeAnalysisResult-method3.8830.0674.109
plot_correlations3.7680.0304.120
plot_gsva_heatmap-ReactomeAnalysisResult-method 79.811 1.611116.086
plot_gsva_heatmap 78.131 1.732115.287
plot_gsva_pathway-ReactomeAnalysisResult-method 77.239 2.108116.606
plot_gsva_pathway 77.791 1.643113.427
plot_gsva_pca-ReactomeAnalysisResult-method 76.751 1.685114.705
plot_gsva_pca 77.874 1.971147.984
plot_heatmap-ReactomeAnalysisResult-method4.3460.0494.544
plot_heatmap4.7710.0294.987
plot_volcano-ReactomeAnalysisResult-method0.3230.0160.351
plot_volcano0.3760.0160.394
print-ReactomeAnalysisRequest-method0.0030.0010.005
print-ReactomeAnalysisResult-method0.2950.0160.312
reactome_links-ReactomeAnalysisResult-method0.3030.0170.355
reactome_links0.2980.0170.317
result_types-ReactomeAnalysisResult-method0.2890.0140.305
result_types0.2830.0160.300
set_method-ReactomeAnalysisRequest-method0.0020.0030.005
set_method0.0040.0030.007
set_parameters-ReactomeAnalysisRequest-method0.0030.0010.004
set_parameters0.0030.0000.003
show-ReactomeAnalysisRequest-method0.0030.0020.005
show-ReactomeAnalysisResult-method0.2900.0160.306