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This page was generated on 2025-09-01 11:43 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-28 13:40 -0400 (Thu, 28 Aug 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ReactomeGSA on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ReactomeGSA
Version: 1.22.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReactomeGSA_1.22.0.tar.gz
StartedAt: 2025-08-29 13:34:20 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 13:51:20 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 1020.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ReactomeGSA_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 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
plot_gsva_heatmap-ReactomeAnalysisResult-method 57.090  3.107  98.916
plot_gsva_heatmap                               52.902  2.570  97.474
plot_gsva_pca-ReactomeAnalysisResult-method     52.647  2.506  91.877
plot_gsva_pathway                               52.820  1.565 103.921
plot_gsva_pca                                   52.598  1.582  92.258
analyse_sc_clusters                             51.199  2.431  96.589
plot_gsva_pathway-ReactomeAnalysisResult-method 50.690  1.588  89.392
analyse_sc_clusters-SingleCellExperiment-method 49.801  1.241 101.778
analyse_sc_clusters-Seurat-method               49.614  0.953  93.697
generate_pseudo_bulk_data                       18.776  1.507  20.544
ReactomeAnalysisRequest                          6.712  0.256   6.991
perform_reactome_analysis                        3.437  0.311  21.780
load_public_dataset                              1.176  0.167  12.274
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  2.039   0.092   2.122 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.7120.2566.991
ReactomeAnalysisResult-class0.2150.0230.242
add_dataset-ReactomeAnalysisRequest-DGEList-method1.0120.0161.031
add_dataset-ReactomeAnalysisRequest-EList-method0.8990.0000.902
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.9230.0160.940
add_dataset-ReactomeAnalysisRequest-data.frame-method1.3140.0241.341
add_dataset-ReactomeAnalysisRequest-matrix-method0.8510.0040.857
add_dataset0.8500.0040.856
analyse_sc_clusters-Seurat-method49.614 0.95393.697
analyse_sc_clusters-SingleCellExperiment-method 49.801 1.241101.778
analyse_sc_clusters51.199 2.43196.589
find_public_datasets0.1400.0354.445
generate_metadata0.0020.0000.002
generate_pseudo_bulk_data18.776 1.50720.544
get_public_species0.0450.0041.077
get_reactome_data_types0.0920.0082.192
get_reactome_methods0.1690.0203.421
get_result-ReactomeAnalysisResult-method0.2430.0120.256
get_result0.2430.0000.244
load_public_dataset 1.176 0.16712.274
names-ReactomeAnalysisResult-method0.2660.0200.287
open_reactome-ReactomeAnalysisResult-method0.2480.0160.265
open_reactome0.2550.0200.275
pathways-ReactomeAnalysisResult-method0.3170.0240.342
pathways0.2660.0120.279
perform_reactome_analysis 3.437 0.31121.780
plot_correlations-ReactomeAnalysisResult-method0.3520.0270.381
plot_correlations0.3080.0310.340
plot_gsva_heatmap-ReactomeAnalysisResult-method57.090 3.10798.916
plot_gsva_heatmap52.902 2.57097.474
plot_gsva_pathway-ReactomeAnalysisResult-method50.690 1.58889.392
plot_gsva_pathway 52.820 1.565103.921
plot_gsva_pca-ReactomeAnalysisResult-method52.647 2.50691.877
plot_gsva_pca52.598 1.58292.258
plot_heatmap-ReactomeAnalysisResult-method0.5430.0480.591
plot_heatmap0.7740.0120.789
plot_volcano-ReactomeAnalysisResult-method0.2560.0160.272
plot_volcano0.2820.0120.295
print-ReactomeAnalysisRequest-method0.0000.0010.002
print-ReactomeAnalysisResult-method0.2420.0080.251
reactome_links-ReactomeAnalysisResult-method0.2400.0080.248
reactome_links0.2500.0040.255
result_types-ReactomeAnalysisResult-method0.2400.0080.250
result_types0.2430.0080.251
set_method-ReactomeAnalysisRequest-method0.0020.0000.002
set_method0.0010.0000.001
set_parameters-ReactomeAnalysisRequest-method0.0020.0000.002
set_parameters0.0010.0000.001
show-ReactomeAnalysisRequest-method0.0010.0000.002
show-ReactomeAnalysisResult-method0.2490.0040.254