Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-24 11:40 -0400 (Tue, 24 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4448 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4453 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4433 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4432 |
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 1679/2260 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.19.0 (landing page) Johannes Griss
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.19.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReactomeGSA_1.19.0.tar.gz |
StartedAt: 2024-09-24 05:05:02 -0400 (Tue, 24 Sep 2024) |
EndedAt: 2024-09-24 05:18:03 -0400 (Tue, 24 Sep 2024) |
EllapsedTime: 780.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReactomeGSA_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.19.0’ * 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 analyse_sc_clusters-Seurat-method 25.388 0.594 57.559 plot_gsva_heatmap-ReactomeAnalysisResult-method 23.514 1.447 54.433 plot_gsva_heatmap 23.227 0.364 52.914 plot_gsva_pathway 22.741 0.350 55.925 plot_gsva_pathway-ReactomeAnalysisResult-method 22.409 0.405 54.398 analyse_sc_clusters 22.325 0.355 54.551 analyse_sc_clusters-SingleCellExperiment-method 22.131 0.434 52.816 plot_gsva_pca 22.181 0.359 55.136 plot_gsva_pca-ReactomeAnalysisResult-method 21.550 0.354 65.929 perform_reactome_analysis 1.818 0.157 14.502 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ReactomeGSA’ ... ** 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” ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 0.995 0.101 1.083
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.206 | 0.233 | 4.451 | |
ReactomeAnalysisResult-class | 1.071 | 0.005 | 1.078 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.750 | 0.000 | 0.751 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.555 | 0.002 | 0.557 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.885 | 0.013 | 0.898 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.514 | 0.003 | 0.517 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.523 | 0.001 | 0.524 | |
add_dataset | 0.520 | 0.001 | 0.521 | |
analyse_sc_clusters-Seurat-method | 25.388 | 0.594 | 57.559 | |
analyse_sc_clusters-SingleCellExperiment-method | 22.131 | 0.434 | 52.816 | |
analyse_sc_clusters | 22.325 | 0.355 | 54.551 | |
find_public_datasets | 0.196 | 0.009 | 3.453 | |
get_public_species | 0.056 | 0.001 | 0.340 | |
get_reactome_data_types | 0.105 | 0.007 | 0.681 | |
get_reactome_methods | 0.168 | 0.370 | 2.036 | |
get_result-ReactomeAnalysisResult-method | 0.115 | 0.004 | 0.120 | |
get_result | 0.104 | 0.009 | 0.113 | |
load_public_dataset | 0.656 | 0.046 | 4.355 | |
names-ReactomeAnalysisResult-method | 0.120 | 0.004 | 0.124 | |
open_reactome-ReactomeAnalysisResult-method | 0.120 | 0.005 | 0.125 | |
open_reactome | 0.121 | 0.005 | 0.127 | |
pathways-ReactomeAnalysisResult-method | 1.489 | 0.055 | 1.544 | |
pathways | 0.915 | 0.003 | 0.918 | |
perform_reactome_analysis | 1.818 | 0.157 | 14.502 | |
plot_correlations-ReactomeAnalysisResult-method | 0.974 | 0.004 | 0.980 | |
plot_correlations | 0.954 | 0.003 | 0.959 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 23.514 | 1.447 | 54.433 | |
plot_gsva_heatmap | 23.227 | 0.364 | 52.914 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 22.409 | 0.405 | 54.398 | |
plot_gsva_pathway | 22.741 | 0.350 | 55.925 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 21.550 | 0.354 | 65.929 | |
plot_gsva_pca | 22.181 | 0.359 | 55.136 | |
plot_heatmap-ReactomeAnalysisResult-method | 1.122 | 0.002 | 1.124 | |
plot_heatmap | 1.223 | 0.001 | 1.224 | |
plot_volcano-ReactomeAnalysisResult-method | 0.121 | 0.002 | 0.123 | |
plot_volcano | 0.152 | 0.001 | 0.154 | |
print-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
print-ReactomeAnalysisResult-method | 0.116 | 0.003 | 0.119 | |
reactome_links-ReactomeAnalysisResult-method | 0.112 | 0.003 | 0.115 | |
reactome_links | 0.109 | 0.003 | 0.113 | |
result_types-ReactomeAnalysisResult-method | 0.114 | 0.002 | 0.116 | |
result_types | 0.116 | 0.000 | 0.116 | |
set_method-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.002 | |
set_method | 0.001 | 0.000 | 0.001 | |
set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
set_parameters | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.112 | 0.001 | 0.113 | |