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This page was generated on 2025-09-25 12:04 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 1722/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 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
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    OK    OK  


CHECK results for ReactomeGSA on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReactomeGSA_1.23.0.tar.gz
StartedAt: 2025-09-25 03:20:57 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 03:39:02 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 1085.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReactomeGSA_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* 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 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
analyse_sc_clusters-Seurat-method               38.561  1.253 131.514
plot_gsva_heatmap-ReactomeAnalysisResult-method 35.363  3.085  74.151
analyse_sc_clusters-SingleCellExperiment-method 35.356  0.961 100.418
plot_gsva_heatmap                               32.650  1.060  64.123
plot_gsva_pathway                               32.634  0.803  69.859
plot_gsva_pathway-ReactomeAnalysisResult-method 32.451  0.915  64.008
plot_gsva_pca                                   32.402  0.849  63.563
plot_gsva_pca-ReactomeAnalysisResult-method     32.459  0.636  63.435
analyse_sc_clusters                             31.356  0.672  70.880
generate_pseudo_bulk_data                       13.966  2.388  16.387
ReactomeAnalysisRequest                          4.968  0.227   5.194
perform_reactome_analysis                        3.320  1.014  17.479
load_public_dataset                              1.416  0.242   5.023
* 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-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 Patched (2025-08-23 r88802) -- "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 
  1.728   0.124   1.839 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest4.9680.2275.194
ReactomeAnalysisResult-class0.1910.0010.191
add_dataset-ReactomeAnalysisRequest-DGEList-method0.9000.0210.922
add_dataset-ReactomeAnalysisRequest-EList-method0.5540.0040.558
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.5470.0310.578
add_dataset-ReactomeAnalysisRequest-data.frame-method0.5420.0030.545
add_dataset-ReactomeAnalysisRequest-matrix-method0.5570.0040.561
add_dataset0.5160.0040.520
analyse_sc_clusters-Seurat-method 38.561 1.253131.514
analyse_sc_clusters-SingleCellExperiment-method 35.356 0.961100.418
analyse_sc_clusters31.356 0.67270.880
find_public_datasets0.4630.0243.689
generate_metadata0.0020.0000.002
generate_pseudo_bulk_data13.966 2.38816.387
get_public_species0.1460.0160.857
get_reactome_data_types0.3860.0611.371
get_reactome_methods0.5330.0642.106
get_result-ReactomeAnalysisResult-method0.5750.1890.763
get_result0.2210.0050.226
load_public_dataset1.4160.2425.023
names-ReactomeAnalysisResult-method0.2290.0210.251
open_reactome-ReactomeAnalysisResult-method0.2210.0190.240
open_reactome0.2300.0190.250
pathways-ReactomeAnalysisResult-method0.3020.0200.321
pathways0.2440.0190.263
perform_reactome_analysis 3.320 1.01417.479
plot_correlations-ReactomeAnalysisResult-method0.3460.0820.429
plot_correlations0.3140.0750.389
plot_gsva_heatmap-ReactomeAnalysisResult-method35.363 3.08574.151
plot_gsva_heatmap32.650 1.06064.123
plot_gsva_pathway-ReactomeAnalysisResult-method32.451 0.91564.008
plot_gsva_pathway32.634 0.80369.859
plot_gsva_pca-ReactomeAnalysisResult-method32.459 0.63663.435
plot_gsva_pca32.402 0.84963.563
plot_heatmap-ReactomeAnalysisResult-method0.5860.0010.588
plot_heatmap0.6690.0060.675
plot_volcano-ReactomeAnalysisResult-method0.2450.0010.247
plot_volcano0.2590.0000.259
print-ReactomeAnalysisRequest-method0.0020.0000.002
print-ReactomeAnalysisResult-method0.2260.0010.227
reactome_links-ReactomeAnalysisResult-method0.2270.0010.228
reactome_links0.2120.0040.216
result_types-ReactomeAnalysisResult-method0.2060.0010.207
result_types0.2120.0030.215
set_method-ReactomeAnalysisRequest-method0.0020.0000.001
set_method0.0010.0000.001
set_parameters-ReactomeAnalysisRequest-method0.0010.0000.001
set_parameters0.0010.0000.001
show-ReactomeAnalysisRequest-method0.0020.0000.002
show-ReactomeAnalysisResult-method0.2360.0010.237