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This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1709/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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
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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


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: 2025-08-15 06:53:06 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 07:07:22 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 856.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 39.22   2.72   76.53
plot_gsva_heatmap                               38.47   2.67   75.04
plot_gsva_pca                                   37.90   2.96   81.25
plot_gsva_pca-ReactomeAnalysisResult-method     37.85   2.97   78.61
analyse_sc_clusters-Seurat-method               37.61   3.11   79.70
analyse_sc_clusters                             37.16   3.08   78.58
plot_gsva_pathway                               35.79   2.90   73.43
analyse_sc_clusters-SingleCellExperiment-method 35.12   2.93   76.48
plot_gsva_pathway-ReactomeAnalysisResult-method 34.72   2.89   72.86
generate_pseudo_bulk_data                       19.02   2.15   22.33
ReactomeAnalysisRequest                          6.47   0.75    7.27
perform_reactome_analysis                        3.93   0.28   18.13
load_public_dataset                              2.21   0.08    5.06
* 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 
   1.96    0.18    2.21 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.470.757.27
ReactomeAnalysisResult-class0.210.050.26
add_dataset-ReactomeAnalysisRequest-DGEList-method1.460.041.50
add_dataset-ReactomeAnalysisRequest-EList-method0.920.060.99
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method1.040.051.09
add_dataset-ReactomeAnalysisRequest-data.frame-method0.890.060.95
add_dataset-ReactomeAnalysisRequest-matrix-method0.890.030.92
add_dataset0.970.020.99
analyse_sc_clusters-Seurat-method37.61 3.1179.70
analyse_sc_clusters-SingleCellExperiment-method35.12 2.9376.48
analyse_sc_clusters37.16 3.0878.58
find_public_datasets0.060.022.42
generate_metadata000
generate_pseudo_bulk_data19.02 2.1522.33
get_public_species0.010.020.42
get_reactome_data_types0.000.020.61
get_reactome_methods0.040.010.97
get_result-ReactomeAnalysisResult-method0.260.020.28
get_result0.220.010.23
load_public_dataset2.210.085.06
names-ReactomeAnalysisResult-method0.240.010.25
open_reactome-ReactomeAnalysisResult-method0.200.060.27
open_reactome0.250.020.26
pathways-ReactomeAnalysisResult-method0.280.050.33
pathways0.220.010.23
perform_reactome_analysis 3.93 0.2818.13
plot_correlations-ReactomeAnalysisResult-method0.240.030.27
plot_correlations0.240.020.25
plot_gsva_heatmap-ReactomeAnalysisResult-method39.22 2.7276.53
plot_gsva_heatmap38.47 2.6775.04
plot_gsva_pathway-ReactomeAnalysisResult-method34.72 2.8972.86
plot_gsva_pathway35.79 2.9073.43
plot_gsva_pca-ReactomeAnalysisResult-method37.85 2.9778.61
plot_gsva_pca37.90 2.9681.25
plot_heatmap-ReactomeAnalysisResult-method0.440.030.50
plot_heatmap0.670.030.98
plot_volcano-ReactomeAnalysisResult-method0.220.030.25
plot_volcano0.270.020.28
print-ReactomeAnalysisRequest-method000
print-ReactomeAnalysisResult-method0.280.030.31
reactome_links-ReactomeAnalysisResult-method0.280.010.30
reactome_links0.270.030.30
result_types-ReactomeAnalysisResult-method0.200.020.21
result_types0.190.010.20
set_method-ReactomeAnalysisRequest-method0.000.020.02
set_method000
set_parameters-ReactomeAnalysisRequest-method000
set_parameters000
show-ReactomeAnalysisRequest-method000
show-ReactomeAnalysisResult-method0.190.030.22