| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-27 11:32 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| 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 1744/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.25.1 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for ReactomeGSA in R Universe. | ||||||||||||||
|
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: 1.25.1 |
| 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_1.25.1.tar.gz |
| StartedAt: 2026-02-27 03:20:53 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 03:26:56 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 362.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: NA |
##############################################################################
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### Running 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_1.25.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReactomeGSA.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.25.1’
* 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 ... ERROR
Running examples in ‘ReactomeGSA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyse_sc_clusters
> ### Title: analyse_sc_clusters
> ### Aliases: analyse_sc_clusters
>
> ### ** Examples
>
> # This example shows how a Seurat object can be analysed
> # the approach is identical for SingleCellExperiment objects
> library(ReactomeGSA.data)
Loading required package: limma
Loading required package: edgeR
Loading required package: Seurat
Loading required package: SeuratObject
Loading required package: sp
Attaching package: ‘SeuratObject’
The following objects are masked from ‘package:base’:
intersect, t
> data(jerby_b_cells)
>
> # perform the GSVA analysis
> gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE)
Converting expression data to string... (This may take a moment)
Conversion complete
Compressing request data...
No encoding supplied: defaulting to UTF-8.
Error in start_reactome_analysis(request = request, compress = compress, :
Request failed (503 - Service Unavailable): Failed to connect to storage system. Please try again in a few minutes.
Calls: analyse_sc_clusters ... analyse_sc_clusters -> .local -> <Anonymous> -> start_reactome_analysis
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyse_sc_clusters-SingleCellExperiment-method 36.584 2.087 77.112
analyse_sc_clusters-Seurat-method 32.140 1.427 59.563
ReactomeAnalysisRequest 4.962 0.235 5.202
* 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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Quitting from analysing-scRNAseq.Rmd:137-140 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `start_reactome_analysis()`:
! Request failed (505 - HTTP Version Not Supported): An unexpected error occurred. The development team was informed. Please try again later.
---
Backtrace:
▆
1. └─ReactomeGSA::perform_reactome_analysis(my_request, compress = FALSE)
2. └─ReactomeGSA::start_reactome_analysis(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics:
Request failed (505 - HTTP Version Not Supported): An unexpected error occurred. The development team was informed. Please try again later.
--- failed 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 `wait_for_loading_dataset()`:
! Request failed (503 - Service Unavailable): The number of analysis requests is currently too high. Please try again in a few minutes.
---
Backtrace:
▆
1. └─ReactomeGSA::load_public_dataset(dataset_search_entry, verbose = TRUE)
2. └─ReactomeGSA:::wait_for_loading_dataset(request, verbose, reactome_url)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'reanalysing-public-data.Rmd' failed with diagnostics:
Request failed (503 - Service Unavailable): The number of analysis requests is currently too high. Please try again in a few minutes.
--- failed re-building ‘reanalysing-public-data.Rmd’
--- re-building ‘using-reactomegsa.Rmd’ using rmarkdown
--- finished re-building ‘using-reactomegsa.Rmd’
SUMMARY: processing the following files failed:
‘analysing-scRNAseq.Rmd’ ‘reanalysing-public-data.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 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 ‘1.25.1’ ** 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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
1.707 0.145 1.840
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 4.962 | 0.235 | 5.202 | |
| ReactomeAnalysisResult-class | 0.188 | 0.005 | 0.192 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.821 | 0.016 | 0.837 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 0.485 | 0.006 | 0.492 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.498 | 0.024 | 0.522 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.518 | 0.005 | 0.523 | |
| add_dataset-ReactomeAnalysisRequest-matrix-method | 0.501 | 0.002 | 0.503 | |
| add_dataset | 0.499 | 0.007 | 0.506 | |
| analyse_sc_clusters-Seurat-method | 32.140 | 1.427 | 59.563 | |
| analyse_sc_clusters-SingleCellExperiment-method | 36.584 | 2.087 | 77.112 | |