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This page was generated on 2025-07-29 12:11 -0400 (Tue, 29 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4516
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 1707/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.23.0  (landing page)
Johannes Griss
Snapshot Date: 2025-07-28 13:25 -0400 (Mon, 28 Jul 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReactomeGSA on kjohnson3

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: /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_1.23.0.tar.gz
StartedAt: 2025-07-28 21:05:28 -0400 (Mon, 28 Jul 2025)
EndedAt: 2025-07-28 21:14:49 -0400 (Mon, 28 Jul 2025)
EllapsedTime: 561.2 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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 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 11.118  0.867  51.485
plot_gsva_pca                                   10.286  1.081  50.158
analyse_sc_clusters-Seurat-method               10.414  0.890  51.790
plot_gsva_heatmap                               10.167  0.987  48.857
plot_gsva_pathway                                9.956  1.024  51.198
plot_gsva_pathway-ReactomeAnalysisResult-method 10.003  0.865  50.036
plot_gsva_pca-ReactomeAnalysisResult-method      9.913  0.924  48.385
analyse_sc_clusters                              9.808  0.962  54.322
analyse_sc_clusters-SingleCellExperiment-method  9.763  0.880  48.626
generate_pseudo_bulk_data                        5.081  0.442   5.546
perform_reactome_analysis                        0.874  0.113  16.030
load_public_dataset                              0.720  0.103  44.366
* 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-3.22-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-arm64/Resources/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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
  0.668   0.061   0.733 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest2.0180.1062.160
ReactomeAnalysisResult-class0.0870.0070.096
add_dataset-ReactomeAnalysisRequest-DGEList-method0.2780.0150.294
add_dataset-ReactomeAnalysisRequest-EList-method0.2790.0220.304
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.2700.0210.292
add_dataset-ReactomeAnalysisRequest-data.frame-method0.2740.0160.289
add_dataset-ReactomeAnalysisRequest-matrix-method0.2770.0260.307
add_dataset0.2770.0260.318
analyse_sc_clusters-Seurat-method10.414 0.89051.790
analyse_sc_clusters-SingleCellExperiment-method 9.763 0.88048.626
analyse_sc_clusters 9.808 0.96254.322
find_public_datasets0.0380.0094.514
generate_metadata0.0010.0000.000
generate_pseudo_bulk_data5.0810.4425.546
get_public_species0.0100.0020.306
get_reactome_data_types0.0210.0030.623
get_reactome_methods0.1620.0171.190
get_result-ReactomeAnalysisResult-method0.0860.0030.089
get_result0.0880.0040.092
load_public_dataset 0.720 0.10344.366
names-ReactomeAnalysisResult-method0.0940.0040.098
open_reactome-ReactomeAnalysisResult-method0.0910.0040.095
open_reactome0.0870.0030.091
pathways-ReactomeAnalysisResult-method0.1070.0030.111
pathways0.1040.0030.107
perform_reactome_analysis 0.874 0.11316.030
plot_correlations-ReactomeAnalysisResult-method0.1130.0040.121
plot_correlations0.1050.0040.110
plot_gsva_heatmap-ReactomeAnalysisResult-method11.118 0.86751.485
plot_gsva_heatmap10.167 0.98748.857
plot_gsva_pathway-ReactomeAnalysisResult-method10.003 0.86550.036
plot_gsva_pathway 9.956 1.02451.198
plot_gsva_pca-ReactomeAnalysisResult-method 9.913 0.92448.385
plot_gsva_pca10.286 1.08150.158
plot_heatmap-ReactomeAnalysisResult-method0.1700.0050.176
plot_heatmap0.1970.0050.203
plot_volcano-ReactomeAnalysisResult-method0.0890.0030.094
plot_volcano0.1080.0030.113
print-ReactomeAnalysisRequest-method0.0010.0010.001
print-ReactomeAnalysisResult-method0.0970.0040.103
reactome_links-ReactomeAnalysisResult-method0.0910.0030.095
reactome_links0.0890.0030.092
result_types-ReactomeAnalysisResult-method0.0950.0030.098
result_types0.0940.0030.106
set_method-ReactomeAnalysisRequest-method0.0010.0000.002
set_method0.0010.0010.001
set_parameters-ReactomeAnalysisRequest-method000
set_parameters0.0010.0000.000
show-ReactomeAnalysisRequest-method0.0000.0000.001
show-ReactomeAnalysisResult-method0.1030.0040.107