Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1732/2346 | 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 | ERROR | skipped | skipped | |||||||||
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. |
Package: ReactomeGSA |
Version: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2025-10-11 03:34:55 -0400 (Sat, 11 Oct 2025) |
EndedAt: 2025-10-11 03:52:52 -0400 (Sat, 11 Oct 2025) |
EllapsedTime: 1077.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * 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 ‘1.23.0’ * 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_heatmap-ReactomeAnalysisResult-method 38.153 1.096 113.398 analyse_sc_clusters-Seurat-method 32.927 0.955 76.665 plot_gsva_heatmap 33.193 0.670 69.409 plot_gsva_pca-ReactomeAnalysisResult-method 32.726 0.978 67.229 plot_gsva_pca 32.261 0.794 72.958 analyse_sc_clusters-SingleCellExperiment-method 31.746 0.724 66.169 plot_gsva_pathway-ReactomeAnalysisResult-method 31.872 0.597 65.870 plot_gsva_pathway 31.560 0.819 65.805 analyse_sc_clusters 30.527 0.578 66.530 generate_pseudo_bulk_data 13.186 0.742 13.952 perform_reactome_analysis 6.875 0.357 53.911 ReactomeAnalysisRequest 4.873 0.230 5.103 load_public_dataset 1.203 0.047 5.795 * 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 ... OK * 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/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 ‘1.23.0’ ** 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 Patched (2025-08-23 r88802) -- "Great Square Root" 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 1.722 0.111 1.821
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.873 | 0.230 | 5.103 | |
ReactomeAnalysisResult-class | 0.204 | 0.004 | 0.209 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.895 | 0.015 | 0.910 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.525 | 0.003 | 0.527 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.511 | 0.028 | 0.539 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.508 | 0.004 | 0.512 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.521 | 0.001 | 0.523 | |
add_dataset | 0.519 | 0.003 | 0.521 | |
analyse_sc_clusters-Seurat-method | 32.927 | 0.955 | 76.665 | |
analyse_sc_clusters-SingleCellExperiment-method | 31.746 | 0.724 | 66.169 | |
analyse_sc_clusters | 30.527 | 0.578 | 66.530 | |
find_public_datasets | 0.481 | 0.022 | 3.092 | |
generate_metadata | 0.000 | 0.001 | 0.001 | |
generate_pseudo_bulk_data | 13.186 | 0.742 | 13.952 | |
get_public_species | 0.157 | 0.008 | 0.662 | |
get_reactome_data_types | 0.391 | 0.021 | 1.610 | |
get_reactome_methods | 0.590 | 0.046 | 2.147 | |
get_result-ReactomeAnalysisResult-method | 0.226 | 0.003 | 0.229 | |
get_result | 0.198 | 0.003 | 0.202 | |
load_public_dataset | 1.203 | 0.047 | 5.795 | |
names-ReactomeAnalysisResult-method | 0.194 | 0.002 | 0.196 | |
open_reactome-ReactomeAnalysisResult-method | 0.206 | 0.002 | 0.208 | |
open_reactome | 0.225 | 0.003 | 0.229 | |
pathways-ReactomeAnalysisResult-method | 0.301 | 0.023 | 0.324 | |
pathways | 0.218 | 0.005 | 0.223 | |
perform_reactome_analysis | 6.875 | 0.357 | 53.911 | |
plot_correlations-ReactomeAnalysisResult-method | 0.344 | 0.004 | 0.348 | |
plot_correlations | 0.264 | 0.000 | 0.264 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 38.153 | 1.096 | 113.398 | |
plot_gsva_heatmap | 33.193 | 0.670 | 69.409 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 31.872 | 0.597 | 65.870 | |
plot_gsva_pathway | 31.560 | 0.819 | 65.805 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 32.726 | 0.978 | 67.229 | |
plot_gsva_pca | 32.261 | 0.794 | 72.958 | |
plot_heatmap-ReactomeAnalysisResult-method | 0.513 | 0.013 | 0.526 | |
plot_heatmap | 0.602 | 0.009 | 0.611 | |
plot_volcano-ReactomeAnalysisResult-method | 0.212 | 0.004 | 0.217 | |
plot_volcano | 0.253 | 0.000 | 0.253 | |
print-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
print-ReactomeAnalysisResult-method | 0.204 | 0.002 | 0.207 | |
reactome_links-ReactomeAnalysisResult-method | 0.202 | 0.000 | 0.201 | |
reactome_links | 0.196 | 0.000 | 0.197 | |
result_types-ReactomeAnalysisResult-method | 0.192 | 0.002 | 0.195 | |
result_types | 0.189 | 0.003 | 0.192 | |
set_method-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
set_method | 0.001 | 0.000 | 0.001 | |
set_parameters-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.001 | |
set_parameters | 0.001 | 0.000 | 0.002 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.203 | 0.001 | 0.204 | |