Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 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 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 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeGSA_1.22.0.tar.gz |
StartedAt: 2025-10-16 02:42:24 -0400 (Thu, 16 Oct 2025) |
EndedAt: 2025-10-16 03:02:46 -0400 (Thu, 16 Oct 2025) |
EllapsedTime: 1222.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ReactomeGSA_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 ‘1.22.0’ * 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 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 36.720 2.497 107.333 plot_gsva_heatmap-ReactomeAnalysisResult-method 36.893 2.249 111.385 plot_gsva_pathway 36.726 2.185 108.979 plot_gsva_heatmap 34.901 2.726 75.711 plot_gsva_pathway-ReactomeAnalysisResult-method 33.167 1.946 69.079 analyse_sc_clusters-Seurat-method 32.992 1.530 80.612 analyse_sc_clusters-SingleCellExperiment-method 31.322 1.465 69.495 analyse_sc_clusters 30.953 1.283 67.954 plot_gsva_pca 25.457 1.307 35.464 generate_pseudo_bulk_data 14.255 1.725 16.035 ReactomeAnalysisRequest 4.854 0.307 5.162 load_public_dataset 4.638 0.298 45.476 perform_reactome_analysis 3.375 0.508 17.226 find_public_datasets 0.457 0.043 5.583 * 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-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "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 1.855 0.124 1.968
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.854 | 0.307 | 5.162 | |
ReactomeAnalysisResult-class | 0.177 | 0.008 | 0.187 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.905 | 0.012 | 0.916 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.528 | 0.012 | 0.541 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.497 | 0.005 | 0.502 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.502 | 0.004 | 0.506 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.509 | 0.002 | 0.511 | |
add_dataset | 0.499 | 0.002 | 0.501 | |
analyse_sc_clusters-Seurat-method | 32.992 | 1.530 | 80.612 | |
analyse_sc_clusters-SingleCellExperiment-method | 31.322 | 1.465 | 69.495 | |
analyse_sc_clusters | 30.953 | 1.283 | 67.954 | |
find_public_datasets | 0.457 | 0.043 | 5.583 | |
generate_metadata | 0.002 | 0.001 | 0.003 | |
generate_pseudo_bulk_data | 14.255 | 1.725 | 16.035 | |
get_public_species | 0.134 | 0.005 | 0.581 | |
get_reactome_data_types | 0.325 | 0.017 | 1.416 | |
get_reactome_methods | 0.386 | 0.030 | 1.835 | |
get_result-ReactomeAnalysisResult-method | 0.276 | 0.037 | 0.314 | |
get_result | 0.221 | 0.006 | 0.228 | |
load_public_dataset | 4.638 | 0.298 | 45.476 | |
names-ReactomeAnalysisResult-method | 0.210 | 0.018 | 0.228 | |
open_reactome-ReactomeAnalysisResult-method | 0.202 | 0.017 | 0.219 | |
open_reactome | 0.228 | 0.012 | 0.239 | |
pathways-ReactomeAnalysisResult-method | 0.259 | 0.029 | 0.288 | |
pathways | 0.231 | 0.019 | 0.250 | |
perform_reactome_analysis | 3.375 | 0.508 | 17.226 | |
plot_correlations-ReactomeAnalysisResult-method | 0.289 | 0.026 | 0.316 | |
plot_correlations | 0.259 | 0.011 | 0.270 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 36.893 | 2.249 | 111.385 | |
plot_gsva_heatmap | 34.901 | 2.726 | 75.711 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 33.167 | 1.946 | 69.079 | |
plot_gsva_pathway | 36.726 | 2.185 | 108.979 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 36.720 | 2.497 | 107.333 | |
plot_gsva_pca | 25.457 | 1.307 | 35.464 | |
plot_heatmap-ReactomeAnalysisResult-method | 0.552 | 0.056 | 0.608 | |
plot_heatmap | 0.645 | 0.058 | 0.704 | |
plot_volcano-ReactomeAnalysisResult-method | 0.231 | 0.022 | 0.253 | |
plot_volcano | 0.240 | 0.011 | 0.252 | |
print-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.211 | 0.013 | 0.224 | |
reactome_links-ReactomeAnalysisResult-method | 0.203 | 0.008 | 0.211 | |
reactome_links | 0.221 | 0.007 | 0.228 | |
result_types-ReactomeAnalysisResult-method | 0.216 | 0.011 | 0.228 | |
result_types | 0.208 | 0.015 | 0.223 | |
set_method-ReactomeAnalysisRequest-method | 0.001 | 0.002 | 0.003 | |
set_method | 0.002 | 0.000 | 0.002 | |
set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.002 | |
set_parameters | 0.002 | 0.000 | 0.002 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
show-ReactomeAnalysisResult-method | 0.229 | 0.010 | 0.240 | |