Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-01 12:07 -0400 (Mon, 01 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1712/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.23.0 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ReactomeGSA |
Version: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2025-08-29 10:39:33 -0000 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 10:57:21 -0000 (Fri, 29 Aug 2025) |
EllapsedTime: 1067.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.23.0’ * 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-ReactomeAnalysisResult-method 57.971 3.260 103.968 plot_gsva_heatmap-ReactomeAnalysisResult-method 56.216 2.996 96.787 plot_gsva_heatmap 55.335 2.667 98.750 plot_gsva_pathway-ReactomeAnalysisResult-method 54.779 2.717 95.525 plot_gsva_pathway 54.217 2.709 98.984 plot_gsva_pca 53.177 3.018 95.932 analyse_sc_clusters-Seurat-method 50.243 1.156 104.986 analyse_sc_clusters 49.745 1.050 92.774 analyse_sc_clusters-SingleCellExperiment-method 49.099 1.627 93.116 generate_pseudo_bulk_data 18.731 1.356 20.247 ReactomeAnalysisRequest 6.582 0.224 6.830 perform_reactome_analysis 4.880 0.503 22.649 load_public_dataset 1.806 0.189 35.001 find_public_datasets 0.152 0.024 7.912 * 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-3.22-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘ReactomeGSA’ ... ** this is package ‘ReactomeGSA’ version ‘1.23.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 2.172 0.109 2.273
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.582 | 0.224 | 6.830 | |
ReactomeAnalysisResult-class | 0.219 | 0.000 | 0.222 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.164 | 0.016 | 1.182 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.863 | 0.008 | 0.872 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.843 | 0.004 | 0.849 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.834 | 0.000 | 0.835 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.854 | 0.007 | 0.863 | |
add_dataset | 0.821 | 0.027 | 0.850 | |
analyse_sc_clusters-Seurat-method | 50.243 | 1.156 | 104.986 | |
analyse_sc_clusters-SingleCellExperiment-method | 49.099 | 1.627 | 93.116 | |
analyse_sc_clusters | 49.745 | 1.050 | 92.774 | |
find_public_datasets | 0.152 | 0.024 | 7.912 | |
generate_metadata | 0.001 | 0.000 | 0.002 | |
generate_pseudo_bulk_data | 18.731 | 1.356 | 20.247 | |
get_public_species | 0.052 | 0.000 | 2.289 | |
get_reactome_data_types | 0.099 | 0.015 | 3.347 | |
get_reactome_methods | 0.163 | 0.012 | 3.907 | |
get_result-ReactomeAnalysisResult-method | 0.261 | 0.024 | 0.286 | |
get_result | 0.254 | 0.008 | 0.263 | |
load_public_dataset | 1.806 | 0.189 | 35.001 | |
names-ReactomeAnalysisResult-method | 0.254 | 0.024 | 0.277 | |
open_reactome-ReactomeAnalysisResult-method | 0.267 | 0.004 | 0.272 | |
open_reactome | 0.255 | 0.024 | 0.279 | |
pathways-ReactomeAnalysisResult-method | 0.342 | 0.012 | 0.354 | |
pathways | 0.275 | 0.004 | 0.280 | |
perform_reactome_analysis | 4.880 | 0.503 | 22.649 | |
plot_correlations-ReactomeAnalysisResult-method | 0.342 | 0.041 | 0.384 | |
plot_correlations | 0.310 | 0.032 | 0.342 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 56.216 | 2.996 | 96.787 | |
plot_gsva_heatmap | 55.335 | 2.667 | 98.750 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 54.779 | 2.717 | 95.525 | |
plot_gsva_pathway | 54.217 | 2.709 | 98.984 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 57.971 | 3.260 | 103.968 | |
plot_gsva_pca | 53.177 | 3.018 | 95.932 | |
plot_heatmap-ReactomeAnalysisResult-method | 0.576 | 0.024 | 0.603 | |
plot_heatmap | 0.758 | 0.048 | 0.808 | |
plot_volcano-ReactomeAnalysisResult-method | 0.281 | 0.000 | 0.282 | |
plot_volcano | 0.285 | 0.016 | 0.301 | |
print-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.248 | 0.012 | 0.260 | |
reactome_links-ReactomeAnalysisResult-method | 0.264 | 0.004 | 0.269 | |
reactome_links | 0.256 | 0.000 | 0.256 | |
result_types-ReactomeAnalysisResult-method | 0.249 | 0.000 | 0.250 | |
result_types | 0.247 | 0.016 | 0.264 | |
set_method-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
set_method | 0.001 | 0.000 | 0.002 | |
set_parameters-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
set_parameters | 0.000 | 0.001 | 0.002 | |
show-ReactomeAnalysisRequest-method | 0.000 | 0.002 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.255 | 0.008 | 0.264 | |