Johannes Griss
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/ReactomeGSA |
| git_branch: devel |
| git_last_commit: 473b5b6 |
| git_last_commit_date: 2025-10-29 10:54:21 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-28 11:38 -0500 (Fri, 28 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| 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 1722/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.25.0 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: ReactomeGSA |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReactomeGSA_1.25.0.tar.gz |
| StartedAt: 2025-11-28 03:07:39 -0500 (Fri, 28 Nov 2025) |
| EndedAt: 2025-11-28 03:23:17 -0500 (Fri, 28 Nov 2025) |
| EllapsedTime: 937.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReactomeGSA_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReactomeGSA.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.25.0’
* 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_pca 34.936 4.564 75.220
analyse_sc_clusters-Seurat-method 35.068 1.644 97.449
analyse_sc_clusters-SingleCellExperiment-method 32.984 2.732 71.134
plot_gsva_heatmap-ReactomeAnalysisResult-method 33.761 1.155 62.024
plot_gsva_heatmap 33.155 0.928 64.035
plot_gsva_pathway-ReactomeAnalysisResult-method 32.788 1.172 59.641
plot_gsva_pca-ReactomeAnalysisResult-method 32.684 0.956 66.545
plot_gsva_pathway 32.292 0.642 67.206
analyse_sc_clusters 24.297 1.228 32.046
generate_pseudo_bulk_data 13.807 1.356 15.167
ReactomeAnalysisRequest 5.069 0.241 5.313
perform_reactome_analysis 4.629 0.324 18.060
load_public_dataset 2.706 0.108 22.567
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown
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--- finished re-building ‘analysing-scRNAseq.Rmd’
--- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown
Quitting from reanalysing-public-data.Rmd:89-94 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fetch_public_data()`:
! Request failed (404 - Not Found): Failed to retrieve dataset. Make sure the dataset was successfully loaded beforehand.
---
Backtrace:
▆
1. └─ReactomeGSA::load_public_dataset(dataset_search_entry, verbose = TRUE)
2. └─ReactomeGSA:::fetch_public_data(dataset_entry, reactome_url)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reanalysing-public-data.Rmd' failed with diagnostics:
Request failed (404 - Not Found): Failed to retrieve dataset. Make sure the dataset was successfully loaded beforehand.
--- failed re-building ‘reanalysing-public-data.Rmd’
--- re-building ‘using-reactomegsa.Rmd’ using rmarkdown
--- finished re-building ‘using-reactomegsa.Rmd’
SUMMARY: processing the following file failed:
‘reanalysing-public-data.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReactomeGSA’ ... ** this is package ‘ReactomeGSA’ version ‘1.25.0’ ** 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)
ReactomeGSA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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
1.742 0.135 1.865
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 5.069 | 0.241 | 5.313 | |
| ReactomeAnalysisResult-class | 0.198 | 0.005 | 0.204 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.920 | 0.015 | 0.935 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 0.526 | 0.003 | 0.529 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.519 | 0.023 | 0.542 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.528 | 0.001 | 0.530 | |
| add_dataset-ReactomeAnalysisRequest-matrix-method | 0.524 | 0.003 | 0.527 | |
| add_dataset | 0.535 | 0.004 | 0.539 | |
| analyse_sc_clusters-Seurat-method | 35.068 | 1.644 | 97.449 | |
| analyse_sc_clusters-SingleCellExperiment-method | 32.984 | 2.732 | 71.134 | |
| analyse_sc_clusters | 24.297 | 1.228 | 32.046 | |
| find_public_datasets | 0.468 | 0.024 | 2.806 | |
| generate_metadata | 0.001 | 0.000 | 0.001 | |
| generate_pseudo_bulk_data | 13.807 | 1.356 | 15.167 | |
| get_public_species | 0.149 | 0.003 | 0.603 | |
| get_reactome_data_types | 0.234 | 0.003 | 1.217 | |
| get_reactome_methods | 0.364 | 0.011 | 1.968 | |
| get_result-ReactomeAnalysisResult-method | 0.260 | 0.023 | 0.283 | |
| get_result | 0.199 | 0.009 | 0.208 | |
| load_public_dataset | 2.706 | 0.108 | 22.567 | |
| names-ReactomeAnalysisResult-method | 0.218 | 0.004 | 0.222 | |
| open_reactome-ReactomeAnalysisResult-method | 0.220 | 0.006 | 0.227 | |
| open_reactome | 0.204 | 0.003 | 0.206 | |
| pathways-ReactomeAnalysisResult-method | 0.253 | 0.010 | 0.263 | |
| pathways | 0.223 | 0.008 | 0.232 | |
| perform_reactome_analysis | 4.629 | 0.324 | 18.060 | |
| plot_correlations-ReactomeAnalysisResult-method | 0.314 | 0.006 | 0.320 | |
| plot_correlations | 0.292 | 0.001 | 0.292 | |
| plot_gsva_heatmap-ReactomeAnalysisResult-method | 33.761 | 1.155 | 62.024 | |
| plot_gsva_heatmap | 33.155 | 0.928 | 64.035 | |
| plot_gsva_pathway-ReactomeAnalysisResult-method | 32.788 | 1.172 | 59.641 | |
| plot_gsva_pathway | 32.292 | 0.642 | 67.206 | |
| plot_gsva_pca-ReactomeAnalysisResult-method | 32.684 | 0.956 | 66.545 | |
| plot_gsva_pca | 34.936 | 4.564 | 75.220 | |
| plot_heatmap-ReactomeAnalysisResult-method | 0.532 | 0.042 | 0.574 | |
| plot_heatmap | 0.620 | 0.015 | 0.635 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.227 | 0.010 | 0.236 | |
| plot_volcano | 0.247 | 0.014 | 0.261 | |
| print-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
| print-ReactomeAnalysisResult-method | 0.214 | 0.008 | 0.222 | |
| reactome_links-ReactomeAnalysisResult-method | 0.204 | 0.008 | 0.212 | |
| reactome_links | 0.215 | 0.004 | 0.219 | |
| result_types-ReactomeAnalysisResult-method | 0.208 | 0.010 | 0.219 | |
| result_types | 0.205 | 0.015 | 0.220 | |
| set_method-ReactomeAnalysisRequest-method | 0.002 | 0.001 | 0.002 | |
| set_method | 0.002 | 0.000 | 0.002 | |
| set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
| set_parameters | 0.000 | 0.001 | 0.001 | |
| show-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.001 | |
| show-ReactomeAnalysisResult-method | 0.211 | 0.004 | 0.215 | |