| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-12 11:57 -0400 (Thu, 12 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4892 |
| 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 1743/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.24.1 (landing page) Johannes Griss
| nebbiolo2 | 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: 1.24.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReactomeGSA_1.24.1.tar.gz |
| StartedAt: 2026-03-12 03:07:11 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 03:23:37 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 985.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ReactomeGSA_1.24.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.24.1’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gsva_heatmap 34.494 1.013 68.362
plot_gsva_heatmap-ReactomeAnalysisResult-method 33.916 0.903 68.286
plot_gsva_pathway 33.751 0.706 69.624
plot_gsva_pca 33.442 0.816 66.924
analyse_sc_clusters-Seurat-method 32.428 1.808 69.679
plot_gsva_pca-ReactomeAnalysisResult-method 33.302 0.823 66.167
analyse_sc_clusters-SingleCellExperiment-method 32.518 1.535 68.060
analyse_sc_clusters 31.690 0.887 66.231
plot_gsva_pathway-ReactomeAnalysisResult-method 31.817 0.529 64.268
generate_pseudo_bulk_data 14.531 0.895 15.444
ReactomeAnalysisRequest 5.013 0.203 5.218
perform_reactome_analysis 4.477 0.261 17.487
load_public_dataset 1.255 0.108 5.009
* 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
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|===== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========= | 13%
|
|=========== | 15%
|
|============ | 17%
|
|============= | 19%
|
|=============== | 21%
|
|================ | 23%
|
|================== | 25%
|
|=================== | 27%
|
|==================== | 29%
|
|====================== | 31%
|
|======================= | 33%
|
|======================== | 35%
|
|========================== | 37%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================== | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|======================================== | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================ | 63%
|
|============================================== | 65%
|
|=============================================== | 67%
|
|================================================ | 69%
|
|================================================== | 71%
|
|=================================================== | 73%
|
|==================================================== | 75%
|
|====================================================== | 77%
|
|======================================================= | 79%
|
|========================================================= | 81%
|
|========================================================== | 83%
|
|=========================================================== | 85%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================= | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
|
| | 0%
|
|=== | 4%
|
|====== | 8%
|
|========= | 12%
|
|============ | 17%
|
|=============== | 21%
|
|================== | 25%
|
|==================== | 29%
|
|======================= | 33%
|
|========================== | 38%
|
|============================= | 42%
|
|================================ | 46%
|
|=================================== | 50%
|
|====================================== | 54%
|
|========================================= | 58%
|
|============================================ | 62%
|
|=============================================== | 67%
|
|================================================== | 71%
|
|==================================================== | 75%
|
|======================================================= | 79%
|
|========================================================== | 83%
|
|============================================================= | 88%
|
|================================================================ | 92%
|
|=================================================================== | 96%
|
|======================================================================| 100%
--- finished re-building ‘analysing-scRNAseq.Rmd’
--- re-building ‘reanalysing-public-data.Rmd’ using rmarkdown
--- finished re-building ‘reanalysing-public-data.Rmd’
--- re-building ‘using-reactomegsa.Rmd’ using rmarkdown
Quitting from using-reactomegsa.Rmd:203-205 [perform_analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Failed to connect to ReactomeGSA at 'https://gsa.reactome.org/: cannot open the connection to 'https://gsa.reactome.org/0.1/methods'. Try reverting the ReactomeGSA url to http://gsa.reactome.org using options(reactome_gsa.url = "http://gsa.reactome.org").
---
Backtrace:
▆
1. └─ReactomeGSA::perform_reactome_analysis(...)
2. └─ReactomeGSA::get_reactome_analysis_result(...)
3. └─ReactomeGSA:::check_reactome_url(reactome_url)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'using-reactomegsa.Rmd' failed with diagnostics:
Failed to connect to ReactomeGSA at 'https://gsa.reactome.org/: cannot open the connection to 'https://gsa.reactome.org/0.1/methods'. Try reverting the ReactomeGSA url to http://gsa.reactome.org using options(reactome_gsa.url = "http://gsa.reactome.org").
--- failed re-building ‘using-reactomegsa.Rmd’
SUMMARY: processing the following file failed:
‘using-reactomegsa.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘ReactomeGSA’ ... ** this is package ‘ReactomeGSA’ version ‘1.24.1’ ** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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
1.713 0.118 1.819
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 5.013 | 0.203 | 5.218 | |
| ReactomeAnalysisResult-class | 0.185 | 0.002 | 0.187 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.902 | 0.015 | 0.917 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 0.546 | 0.000 | 0.546 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.547 | 0.024 | 0.571 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.529 | 0.006 | 0.534 | |
| add_dataset-ReactomeAnalysisRequest-matrix-method | 0.547 | 0.005 | 0.552 | |
| add_dataset | 0.540 | 0.002 | 0.542 | |
| analyse_sc_clusters-Seurat-method | 32.428 | 1.808 | 69.679 | |
| analyse_sc_clusters-SingleCellExperiment-method | 32.518 | 1.535 | 68.060 | |
| analyse_sc_clusters | 31.690 | 0.887 | 66.231 | |
| find_public_datasets | 0.512 | 0.042 | 3.218 | |
| generate_metadata | 0.003 | 0.000 | 0.003 | |
| generate_pseudo_bulk_data | 14.531 | 0.895 | 15.444 | |
| get_public_species | 0.150 | 0.011 | 0.676 | |
| get_reactome_data_types | 0.355 | 0.019 | 1.405 | |
| get_reactome_methods | 0.594 | 0.035 | 2.380 | |
| get_result-ReactomeAnalysisResult-method | 0.231 | 0.007 | 0.237 | |
| get_result | 0.188 | 0.003 | 0.191 | |
| load_public_dataset | 1.255 | 0.108 | 5.009 | |
| names-ReactomeAnalysisResult-method | 0.200 | 0.011 | 0.211 | |
| open_reactome-ReactomeAnalysisResult-method | 0.209 | 0.006 | 0.215 | |
| open_reactome | 0.224 | 0.003 | 0.227 | |
| pathways-ReactomeAnalysisResult-method | 0.273 | 0.004 | 0.277 | |
| pathways | 0.214 | 0.003 | 0.218 | |
| perform_reactome_analysis | 4.477 | 0.261 | 17.487 | |
| plot_correlations-ReactomeAnalysisResult-method | 0.282 | 0.006 | 0.289 | |
| plot_correlations | 0.245 | 0.003 | 0.249 | |
| plot_gsva_heatmap-ReactomeAnalysisResult-method | 33.916 | 0.903 | 68.286 | |
| plot_gsva_heatmap | 34.494 | 1.013 | 68.362 | |
| plot_gsva_pathway-ReactomeAnalysisResult-method | 31.817 | 0.529 | 64.268 | |
| plot_gsva_pathway | 33.751 | 0.706 | 69.624 | |
| plot_gsva_pca-ReactomeAnalysisResult-method | 33.302 | 0.823 | 66.167 | |
| plot_gsva_pca | 33.442 | 0.816 | 66.924 | |
| plot_heatmap-ReactomeAnalysisResult-method | 0.508 | 0.003 | 0.511 | |
| plot_heatmap | 0.631 | 0.001 | 0.632 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.231 | 0.002 | 0.233 | |
| plot_volcano | 0.245 | 0.005 | 0.250 | |
| print-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.001 | |
| print-ReactomeAnalysisResult-method | 0.202 | 0.009 | 0.211 | |
| reactome_links-ReactomeAnalysisResult-method | 0.201 | 0.008 | 0.209 | |
| reactome_links | 0.193 | 0.005 | 0.198 | |
| result_types-ReactomeAnalysisResult-method | 0.199 | 0.007 | 0.206 | |
| result_types | 0.206 | 0.004 | 0.210 | |
| set_method-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.002 | |
| set_method | 0.001 | 0.000 | 0.001 | |
| set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
| set_parameters | 0.001 | 0.000 | 0.001 | |
| show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
| show-ReactomeAnalysisResult-method | 0.198 | 0.003 | 0.201 | |