Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
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 1728/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.22.0 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.22.0 |
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: 2025-09-24 08:19:47 -0400 (Wed, 24 Sep 2025) |
EndedAt: 2025-09-24 08:35:19 -0400 (Wed, 24 Sep 2025) |
EllapsedTime: 931.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * 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 analyse_sc_clusters-Seurat-method 32.338 2.553 75.714 analyse_sc_clusters 31.085 3.105 105.994 analyse_sc_clusters-SingleCellExperiment-method 31.593 2.540 75.456 plot_gsva_heatmap-ReactomeAnalysisResult-method 30.669 2.199 71.056 plot_gsva_pathway 30.438 2.376 105.087 plot_gsva_heatmap 30.454 2.231 67.442 plot_gsva_pca 29.727 2.307 74.154 plot_gsva_pca-ReactomeAnalysisResult-method 28.569 3.016 75.008 plot_gsva_pathway-ReactomeAnalysisResult-method 28.373 2.008 82.226 generate_pseudo_bulk_data 16.249 1.523 18.077 ReactomeAnalysisRequest 6.165 0.437 6.713 perform_reactome_analysis 2.242 0.233 45.660 load_public_dataset 1.686 0.149 29.233 * 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.
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)
ReactomeGSA.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 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 2.122 0.221 2.355
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.165 | 0.437 | 6.713 | |
ReactomeAnalysisResult-class | 0.295 | 0.016 | 0.315 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.283 | 0.073 | 1.370 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.799 | 0.058 | 0.862 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.819 | 0.061 | 0.888 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.814 | 0.054 | 0.872 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.819 | 0.051 | 0.878 | |
add_dataset | 0.797 | 0.054 | 0.859 | |
analyse_sc_clusters-Seurat-method | 32.338 | 2.553 | 75.714 | |
analyse_sc_clusters-SingleCellExperiment-method | 31.593 | 2.540 | 75.456 | |
analyse_sc_clusters | 31.085 | 3.105 | 105.994 | |
find_public_datasets | 0.118 | 0.016 | 2.409 | |
generate_metadata | 0.001 | 0.000 | 0.002 | |
generate_pseudo_bulk_data | 16.249 | 1.523 | 18.077 | |
get_public_species | 0.033 | 0.005 | 0.669 | |
get_reactome_data_types | 0.066 | 0.009 | 0.583 | |
get_reactome_methods | 0.109 | 0.017 | 0.775 | |
get_result-ReactomeAnalysisResult-method | 0.316 | 0.011 | 0.327 | |
get_result | 0.295 | 0.013 | 0.309 | |
load_public_dataset | 1.686 | 0.149 | 29.233 | |
names-ReactomeAnalysisResult-method | 0.292 | 0.012 | 0.304 | |
open_reactome-ReactomeAnalysisResult-method | 0.282 | 0.012 | 0.295 | |
open_reactome | 0.280 | 0.010 | 0.292 | |
pathways-ReactomeAnalysisResult-method | 0.369 | 0.019 | 0.388 | |
pathways | 0.329 | 0.014 | 0.343 | |
perform_reactome_analysis | 2.242 | 0.233 | 45.660 | |
plot_correlations-ReactomeAnalysisResult-method | 0.401 | 0.021 | 0.430 | |
plot_correlations | 0.368 | 0.017 | 0.389 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 30.669 | 2.199 | 71.056 | |
plot_gsva_heatmap | 30.454 | 2.231 | 67.442 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 28.373 | 2.008 | 82.226 | |
plot_gsva_pathway | 30.438 | 2.376 | 105.087 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 28.569 | 3.016 | 75.008 | |
plot_gsva_pca | 29.727 | 2.307 | 74.154 | |
plot_heatmap-ReactomeAnalysisResult-method | 0.639 | 0.023 | 0.666 | |
plot_heatmap | 0.730 | 0.018 | 0.748 | |
plot_volcano-ReactomeAnalysisResult-method | 0.305 | 0.014 | 0.325 | |
plot_volcano | 0.326 | 0.016 | 0.343 | |
print-ReactomeAnalysisRequest-method | 0.002 | 0.001 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.295 | 0.015 | 0.309 | |
reactome_links-ReactomeAnalysisResult-method | 0.290 | 0.014 | 0.304 | |
reactome_links | 0.296 | 0.014 | 0.310 | |
result_types-ReactomeAnalysisResult-method | 0.302 | 0.015 | 0.317 | |
result_types | 0.305 | 0.014 | 0.319 | |
set_method-ReactomeAnalysisRequest-method | 0.002 | 0.002 | 0.004 | |
set_method | 0.002 | 0.002 | 0.004 | |
set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
set_parameters | 0.002 | 0.000 | 0.002 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.298 | 0.016 | 0.314 | |