Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-01 11:43 -0400 (Mon, 01 Sep 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" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ReactomeGSA |
Version: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2025-08-29 13:34:20 -0000 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 13:51:20 -0000 (Fri, 29 Aug 2025) |
EllapsedTime: 1020.8 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * 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 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 57.090 3.107 98.916 plot_gsva_heatmap 52.902 2.570 97.474 plot_gsva_pca-ReactomeAnalysisResult-method 52.647 2.506 91.877 plot_gsva_pathway 52.820 1.565 103.921 plot_gsva_pca 52.598 1.582 92.258 analyse_sc_clusters 51.199 2.431 96.589 plot_gsva_pathway-ReactomeAnalysisResult-method 50.690 1.588 89.392 analyse_sc_clusters-SingleCellExperiment-method 49.801 1.241 101.778 analyse_sc_clusters-Seurat-method 49.614 0.953 93.697 generate_pseudo_bulk_data 18.776 1.507 20.544 ReactomeAnalysisRequest 6.712 0.256 6.991 perform_reactome_analysis 3.437 0.311 21.780 load_public_dataset 1.176 0.167 12.274 * 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-3.21-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-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 2.039 0.092 2.122
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.712 | 0.256 | 6.991 | |
ReactomeAnalysisResult-class | 0.215 | 0.023 | 0.242 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.012 | 0.016 | 1.031 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.899 | 0.000 | 0.902 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.923 | 0.016 | 0.940 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.314 | 0.024 | 1.341 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.851 | 0.004 | 0.857 | |
add_dataset | 0.850 | 0.004 | 0.856 | |
analyse_sc_clusters-Seurat-method | 49.614 | 0.953 | 93.697 | |
analyse_sc_clusters-SingleCellExperiment-method | 49.801 | 1.241 | 101.778 | |
analyse_sc_clusters | 51.199 | 2.431 | 96.589 | |
find_public_datasets | 0.140 | 0.035 | 4.445 | |
generate_metadata | 0.002 | 0.000 | 0.002 | |
generate_pseudo_bulk_data | 18.776 | 1.507 | 20.544 | |
get_public_species | 0.045 | 0.004 | 1.077 | |
get_reactome_data_types | 0.092 | 0.008 | 2.192 | |
get_reactome_methods | 0.169 | 0.020 | 3.421 | |
get_result-ReactomeAnalysisResult-method | 0.243 | 0.012 | 0.256 | |
get_result | 0.243 | 0.000 | 0.244 | |
load_public_dataset | 1.176 | 0.167 | 12.274 | |
names-ReactomeAnalysisResult-method | 0.266 | 0.020 | 0.287 | |
open_reactome-ReactomeAnalysisResult-method | 0.248 | 0.016 | 0.265 | |
open_reactome | 0.255 | 0.020 | 0.275 | |
pathways-ReactomeAnalysisResult-method | 0.317 | 0.024 | 0.342 | |
pathways | 0.266 | 0.012 | 0.279 | |
perform_reactome_analysis | 3.437 | 0.311 | 21.780 | |
plot_correlations-ReactomeAnalysisResult-method | 0.352 | 0.027 | 0.381 | |
plot_correlations | 0.308 | 0.031 | 0.340 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 57.090 | 3.107 | 98.916 | |
plot_gsva_heatmap | 52.902 | 2.570 | 97.474 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 50.690 | 1.588 | 89.392 | |
plot_gsva_pathway | 52.820 | 1.565 | 103.921 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 52.647 | 2.506 | 91.877 | |
plot_gsva_pca | 52.598 | 1.582 | 92.258 | |
plot_heatmap-ReactomeAnalysisResult-method | 0.543 | 0.048 | 0.591 | |
plot_heatmap | 0.774 | 0.012 | 0.789 | |
plot_volcano-ReactomeAnalysisResult-method | 0.256 | 0.016 | 0.272 | |
plot_volcano | 0.282 | 0.012 | 0.295 | |
print-ReactomeAnalysisRequest-method | 0.000 | 0.001 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.242 | 0.008 | 0.251 | |
reactome_links-ReactomeAnalysisResult-method | 0.240 | 0.008 | 0.248 | |
reactome_links | 0.250 | 0.004 | 0.255 | |
result_types-ReactomeAnalysisResult-method | 0.240 | 0.008 | 0.250 | |
result_types | 0.243 | 0.008 | 0.251 | |
set_method-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
set_method | 0.001 | 0.000 | 0.001 | |
set_parameters-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
set_parameters | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
show-ReactomeAnalysisResult-method | 0.249 | 0.004 | 0.254 | |