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This page was generated on 2025-04-21 11:46 -0400 (Mon, 21 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1728/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.22.0  (landing page)
Johannes Griss
Snapshot Date: 2025-04-20 13:40 -0400 (Sun, 20 Apr 2025)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_21
git_last_commit: 6e8adbb
git_last_commit_date: 2025-04-15 11:49:59 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


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: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2025-04-20 21:11:31 -0400 (Sun, 20 Apr 2025)
EndedAt: 2025-04-20 21:20:44 -0400 (Sun, 20 Apr 2025)
EllapsedTime: 553.0 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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 ‘1.22.0’
* 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 11.724  0.915  43.213
plot_gsva_heatmap                               10.503  1.206  81.737
plot_gsva_pathway-ReactomeAnalysisResult-method 10.337  1.266  83.951
plot_gsva_pca                                   10.324  1.189  42.531
plot_gsva_pathway                               10.012  1.135  42.580
plot_gsva_pca-ReactomeAnalysisResult-method      9.974  1.021  41.481
analyse_sc_clusters-Seurat-method               10.074  0.854  41.092
analyse_sc_clusters                              9.537  1.004  41.444
analyse_sc_clusters-SingleCellExperiment-method  9.645  0.851  41.935
generate_pseudo_bulk_data                        5.304  0.481   5.864
perform_reactome_analysis                        0.908  0.111  13.444
load_public_dataset                              0.615  0.085  36.175
* 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-3.21-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 ‘1.22.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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 
  0.697   0.069   0.760 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest1.8710.1121.991
ReactomeAnalysisResult-class0.0830.0040.088
add_dataset-ReactomeAnalysisRequest-DGEList-method0.3280.0360.364
add_dataset-ReactomeAnalysisRequest-EList-method0.2700.0230.294
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.2690.0190.289
add_dataset-ReactomeAnalysisRequest-data.frame-method0.4190.0340.453
add_dataset-ReactomeAnalysisRequest-matrix-method0.2530.0220.276
add_dataset0.2500.0180.268
analyse_sc_clusters-Seurat-method10.074 0.85441.092
analyse_sc_clusters-SingleCellExperiment-method 9.645 0.85141.935
analyse_sc_clusters 9.537 1.00441.444
find_public_datasets0.0390.0062.174
generate_metadata0.0000.0000.001
generate_pseudo_bulk_data5.3040.4815.864
get_public_species0.0110.0020.287
get_reactome_data_types0.0210.0030.556
get_reactome_methods0.0360.0050.933
get_result-ReactomeAnalysisResult-method0.0980.0040.104
get_result0.0830.0040.087
load_public_dataset 0.615 0.08536.175
names-ReactomeAnalysisResult-method0.0850.0030.090
open_reactome-ReactomeAnalysisResult-method0.0900.0030.093
open_reactome0.0870.0040.090
pathways-ReactomeAnalysisResult-method0.1070.0050.112
pathways0.0910.0040.096
perform_reactome_analysis 0.908 0.11113.444
plot_correlations-ReactomeAnalysisResult-method0.1140.0040.118
plot_correlations0.1040.0030.108
plot_gsva_heatmap-ReactomeAnalysisResult-method11.724 0.91543.213
plot_gsva_heatmap10.503 1.20681.737
plot_gsva_pathway-ReactomeAnalysisResult-method10.337 1.26683.951
plot_gsva_pathway10.012 1.13542.580
plot_gsva_pca-ReactomeAnalysisResult-method 9.974 1.02141.481
plot_gsva_pca10.324 1.18942.531
plot_heatmap-ReactomeAnalysisResult-method0.1750.0050.195
plot_heatmap0.2080.0040.213
plot_volcano-ReactomeAnalysisResult-method0.0870.0030.090
plot_volcano0.0950.0030.107
print-ReactomeAnalysisRequest-method0.0010.0010.001
print-ReactomeAnalysisResult-method0.0930.0030.112
reactome_links-ReactomeAnalysisResult-method0.0930.0030.097
reactome_links0.0930.0030.096
result_types-ReactomeAnalysisResult-method0.0960.0030.099
result_types0.0880.0030.096
set_method-ReactomeAnalysisRequest-method0.0000.0000.001
set_method0.0000.0010.001
set_parameters-ReactomeAnalysisRequest-method0.0010.0000.001
set_parameters000
show-ReactomeAnalysisRequest-method0.0010.0010.000
show-ReactomeAnalysisResult-method0.0890.0040.102