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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1707/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-08-06 14:04 -0400 (Wed, 06 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 24.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ReactomeGSA on palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings ReactomeGSA_1.23.0.tar.gz
StartedAt: 2025-08-07 05:47:04 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 06:02:16 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 912.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings ReactomeGSA_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 40.20   2.84   77.77
analyse_sc_clusters-Seurat-method               39.06   2.66   83.65
analyse_sc_clusters                             36.95   3.50   78.78
plot_gsva_pathway                               37.23   3.06   73.81
plot_gsva_pca-ReactomeAnalysisResult-method     36.72   3.16   85.74
plot_gsva_pca                                   36.64   2.69   80.05
plot_gsva_heatmap                               36.17   2.77   76.75
analyse_sc_clusters-SingleCellExperiment-method 35.43   2.97   80.35
plot_gsva_pathway-ReactomeAnalysisResult-method 35.08   2.78   72.94
generate_pseudo_bulk_data                       18.44   2.33   22.00
ReactomeAnalysisRequest                          6.13   0.44    6.65
perform_reactome_analysis                        3.99   0.36   17.59
load_public_dataset                              2.49   0.24   42.55
* 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
  'F:/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
   2.01    0.28    2.35 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.130.446.65
ReactomeAnalysisResult-class0.260.010.30
add_dataset-ReactomeAnalysisRequest-DGEList-method1.390.101.49
add_dataset-ReactomeAnalysisRequest-EList-method0.930.010.95
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.960.101.05
add_dataset-ReactomeAnalysisRequest-data.frame-method0.940.010.95
add_dataset-ReactomeAnalysisRequest-matrix-method0.920.101.02
add_dataset0.830.100.94
analyse_sc_clusters-Seurat-method39.06 2.6683.65
analyse_sc_clusters-SingleCellExperiment-method35.43 2.9780.35
analyse_sc_clusters36.95 3.5078.78
find_public_datasets0.010.002.00
generate_metadata000
generate_pseudo_bulk_data18.44 2.3322.00
get_public_species0.000.010.43
get_reactome_data_types0.000.050.59
get_reactome_methods0.050.000.94
get_result-ReactomeAnalysisResult-method0.280.030.31
get_result0.270.030.30
load_public_dataset 2.49 0.2442.55
names-ReactomeAnalysisResult-method0.170.040.22
open_reactome-ReactomeAnalysisResult-method0.280.000.28
open_reactome0.160.040.19
pathways-ReactomeAnalysisResult-method0.230.010.25
pathways0.230.050.28
perform_reactome_analysis 3.99 0.3617.59
plot_correlations-ReactomeAnalysisResult-method0.310.010.33
plot_correlations0.300.020.31
plot_gsva_heatmap-ReactomeAnalysisResult-method40.20 2.8477.77
plot_gsva_heatmap36.17 2.7776.75
plot_gsva_pathway-ReactomeAnalysisResult-method35.08 2.7872.94
plot_gsva_pathway37.23 3.0673.81
plot_gsva_pca-ReactomeAnalysisResult-method36.72 3.1685.74
plot_gsva_pca36.64 2.6980.05
plot_heatmap-ReactomeAnalysisResult-method0.540.060.61
plot_heatmap0.700.010.72
plot_volcano-ReactomeAnalysisResult-method0.310.000.31
plot_volcano0.250.030.28
print-ReactomeAnalysisRequest-method000
print-ReactomeAnalysisResult-method0.280.020.30
reactome_links-ReactomeAnalysisResult-method0.260.030.29
reactome_links0.220.000.22
result_types-ReactomeAnalysisResult-method0.220.020.24
result_types0.220.010.23
set_method-ReactomeAnalysisRequest-method0.000.000.02
set_method0.000.020.01
set_parameters-ReactomeAnalysisRequest-method000
set_parameters000
show-ReactomeAnalysisRequest-method000
show-ReactomeAnalysisResult-method0.220.010.23