Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-07-23 12:09 -0400 (Wed, 23 Jul 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4792 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4530 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4573 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4514 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4510 |
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 1706/2311 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.23.0 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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. |
Package: ReactomeGSA |
Version: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2025-07-22 23:07:03 -0400 (Tue, 22 Jul 2025) |
EndedAt: 2025-07-22 23:22:03 -0400 (Tue, 22 Jul 2025) |
EllapsedTime: 899.8 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 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-ReactomeAnalysisResult-method 38.420 1.646 72.664 analyse_sc_clusters-Seurat-method 37.298 1.521 71.406 plot_gsva_pca-ReactomeAnalysisResult-method 36.496 1.695 71.068 plot_gsva_heatmap 36.352 1.688 70.812 analyse_sc_clusters 35.962 1.490 115.864 plot_gsva_pathway 35.690 1.744 68.317 analyse_sc_clusters-SingleCellExperiment-method 35.888 1.464 69.046 plot_gsva_pathway-ReactomeAnalysisResult-method 34.842 1.729 69.489 plot_gsva_pca 34.521 1.661 66.765 generate_pseudo_bulk_data 14.886 1.848 16.912 ReactomeAnalysisRequest 6.146 0.363 6.557 perform_reactome_analysis 3.228 0.281 57.739 load_public_dataset 1.930 0.176 46.453 * 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-3.22-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-x86_64/Resources/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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 1.867 0.186 2.054
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.146 | 0.363 | 6.557 | |
ReactomeAnalysisResult-class | 0.240 | 0.016 | 0.259 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.796 | 0.056 | 0.861 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.831 | 0.039 | 0.878 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.806 | 0.045 | 0.858 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.769 | 0.053 | 0.826 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.799 | 0.039 | 0.842 | |
add_dataset | 0.786 | 0.036 | 0.828 | |
analyse_sc_clusters-Seurat-method | 37.298 | 1.521 | 71.406 | |
analyse_sc_clusters-SingleCellExperiment-method | 35.888 | 1.464 | 69.046 | |
analyse_sc_clusters | 35.962 | 1.490 | 115.864 | |
find_public_datasets | 0.095 | 0.015 | 3.218 | |
generate_metadata | 0.001 | 0.000 | 0.001 | |
generate_pseudo_bulk_data | 14.886 | 1.848 | 16.912 | |
get_public_species | 0.030 | 0.003 | 0.315 | |
get_reactome_data_types | 0.055 | 0.006 | 0.636 | |
get_reactome_methods | 0.379 | 0.072 | 1.347 | |
get_result-ReactomeAnalysisResult-method | 0.210 | 0.010 | 0.223 | |
get_result | 0.227 | 0.010 | 0.237 | |
load_public_dataset | 1.930 | 0.176 | 46.453 | |
names-ReactomeAnalysisResult-method | 0.223 | 0.011 | 0.238 | |
open_reactome-ReactomeAnalysisResult-method | 0.224 | 0.011 | 0.236 | |
open_reactome | 0.232 | 0.010 | 0.245 | |
pathways-ReactomeAnalysisResult-method | 0.309 | 0.012 | 0.325 | |
pathways | 0.275 | 0.012 | 0.290 | |
perform_reactome_analysis | 3.228 | 0.281 | 57.739 | |
plot_correlations-ReactomeAnalysisResult-method | 0.303 | 0.010 | 0.319 | |
plot_correlations | 0.297 | 0.010 | 0.309 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 38.420 | 1.646 | 72.664 | |
plot_gsva_heatmap | 36.352 | 1.688 | 70.812 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 34.842 | 1.729 | 69.489 | |
plot_gsva_pathway | 35.690 | 1.744 | 68.317 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 36.496 | 1.695 | 71.068 | |
plot_gsva_pca | 34.521 | 1.661 | 66.765 | |
plot_heatmap-ReactomeAnalysisResult-method | 0.486 | 0.015 | 0.506 | |
plot_heatmap | 0.619 | 0.013 | 0.635 | |
plot_volcano-ReactomeAnalysisResult-method | 0.247 | 0.009 | 0.258 | |
plot_volcano | 0.274 | 0.011 | 0.288 | |
print-ReactomeAnalysisRequest-method | 0.002 | 0.001 | 0.003 | |
print-ReactomeAnalysisResult-method | 0.219 | 0.009 | 0.228 | |
reactome_links-ReactomeAnalysisResult-method | 0.238 | 0.010 | 0.248 | |
reactome_links | 0.236 | 0.010 | 0.247 | |
result_types-ReactomeAnalysisResult-method | 0.223 | 0.010 | 0.232 | |
result_types | 0.238 | 0.010 | 0.250 | |
set_method-ReactomeAnalysisRequest-method | 0.002 | 0.002 | 0.005 | |
set_method | 0.002 | 0.002 | 0.003 | |
set_parameters-ReactomeAnalysisRequest-method | 0.002 | 0.001 | 0.002 | |
set_parameters | 0.001 | 0.001 | 0.002 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.002 | |
show-ReactomeAnalysisResult-method | 0.240 | 0.010 | 0.251 | |