Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-02 11:42 -0400 (Thu, 02 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" | 4831 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
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 | 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. - 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: 2025-09-30 13:33:34 -0000 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 13:47:36 -0000 (Tue, 30 Sep 2025) |
EllapsedTime: 842.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ReactomeGSA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 ... ERROR Running examples in ‘ReactomeGSA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_gsva_pathway,ReactomeAnalysisResult-method > ### Title: ReactomeAnalysisResult - plot_gsva_pathway > ### Aliases: plot_gsva_pathway,ReactomeAnalysisResult-method > > ### ** Examples > > # load the scRNA-seq example data > library(ReactomeGSA.data) Loading required package: limma Loading required package: edgeR Loading required package: Seurat Loading required package: SeuratObject Loading required package: sp 'SeuratObject' was built with package 'Matrix' 1.7.2 but the current version is 1.7.3; it is recomended that you reinstall 'SeuratObject' as the ABI for 'Matrix' may have changed Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t > data(jerby_b_cells) > > # perform the GSVA analysis > gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE) Converting expression data to string... (This may take a moment) Conversion complete Compressing request data... Reactome Analysis submitted succesfully > > # create the plot > plot_obj <- plot_gsva_pathway(gsva_result, "R-HSA-389542") Error: C stack usage 7970848 is too close to the limit Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_gsva_heatmap-ReactomeAnalysisResult-method 59.223 3.178 106.656 plot_gsva_heatmap 56.044 1.968 101.657 analyse_sc_clusters 50.379 0.826 133.065 analyse_sc_clusters-Seurat-method 49.893 0.620 101.321 analyse_sc_clusters-SingleCellExperiment-method 49.640 0.760 97.536 generate_pseudo_bulk_data 18.729 1.143 24.067 ReactomeAnalysisRequest 6.806 0.287 8.733 perform_reactome_analysis 4.178 0.237 61.757 load_public_dataset 1.959 0.142 45.085 find_public_datasets 0.155 0.014 6.154 * 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 ERROR, 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 2.053 0.078 2.384
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.806 | 0.287 | 8.733 | |
ReactomeAnalysisResult-class | 0.228 | 0.004 | 0.365 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.013 | 0.012 | 1.087 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.905 | 0.016 | 1.015 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.913 | 0.029 | 1.004 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.308 | 0.018 | 1.333 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.858 | 0.004 | 0.919 | |
add_dataset | 0.857 | 0.000 | 0.875 | |
analyse_sc_clusters-Seurat-method | 49.893 | 0.620 | 101.321 | |
analyse_sc_clusters-SingleCellExperiment-method | 49.640 | 0.760 | 97.536 | |
analyse_sc_clusters | 50.379 | 0.826 | 133.065 | |
find_public_datasets | 0.155 | 0.014 | 6.154 | |
generate_metadata | 0.002 | 0.000 | 0.002 | |
generate_pseudo_bulk_data | 18.729 | 1.143 | 24.067 | |
get_public_species | 0.050 | 0.008 | 1.574 | |
get_reactome_data_types | 0.109 | 0.005 | 3.111 | |
get_reactome_methods | 0.161 | 0.012 | 3.404 | |
get_result-ReactomeAnalysisResult-method | 0.259 | 0.012 | 0.559 | |
get_result | 0.247 | 0.012 | 0.260 | |
load_public_dataset | 1.959 | 0.142 | 45.085 | |
names-ReactomeAnalysisResult-method | 0.254 | 0.024 | 0.406 | |
open_reactome-ReactomeAnalysisResult-method | 0.247 | 0.008 | 0.256 | |
open_reactome | 0.254 | 0.008 | 0.262 | |
pathways-ReactomeAnalysisResult-method | 0.336 | 0.020 | 0.357 | |
pathways | 0.302 | 0.048 | 0.388 | |
perform_reactome_analysis | 4.178 | 0.237 | 61.757 | |
plot_correlations-ReactomeAnalysisResult-method | 0.345 | 0.032 | 0.378 | |
plot_correlations | 0.377 | 0.033 | 0.411 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 59.223 | 3.178 | 106.656 | |
plot_gsva_heatmap | 56.044 | 1.968 | 101.657 | |