Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1713/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.18.0 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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: 1.18.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReactomeGSA_1.18.0.tar.gz |
StartedAt: 2024-06-24 02:58:11 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 03:14:31 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 980.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReactomeGSA_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.18.0’ * 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 33.833 0.544 75.450 plot_gsva_heatmap 33.783 0.548 76.056 analyse_sc_clusters-Seurat-method 32.718 0.954 74.935 plot_gsva_pathway 32.513 0.879 74.492 analyse_sc_clusters-SingleCellExperiment-method 32.403 0.863 73.492 plot_gsva_pathway-ReactomeAnalysisResult-method 32.139 0.762 73.495 plot_gsva_pca 32.321 0.570 74.493 analyse_sc_clusters 31.931 0.552 73.734 plot_gsva_pca-ReactomeAnalysisResult-method 31.376 0.651 72.902 perform_reactome_analysis 3.068 0.039 16.551 * 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-3.19-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 1.542 0.061 1.591
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.704 | 0.263 | 4.969 | |
ReactomeAnalysisResult-class | 1.237 | 0.016 | 1.254 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.746 | 0.024 | 0.770 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.643 | 0.012 | 0.654 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.639 | 0.004 | 0.642 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.951 | 0.028 | 0.978 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.620 | 0.024 | 0.644 | |
add_dataset | 0.639 | 0.004 | 0.644 | |
analyse_sc_clusters-Seurat-method | 32.718 | 0.954 | 74.935 | |
analyse_sc_clusters-SingleCellExperiment-method | 32.403 | 0.863 | 73.492 | |
analyse_sc_clusters | 31.931 | 0.552 | 73.734 | |
find_public_datasets | 0.521 | 0.016 | 3.025 | |
get_public_species | 0.202 | 0.000 | 0.816 | |
get_reactome_data_types | 0.291 | 0.008 | 1.326 | |
get_reactome_methods | 0.484 | 0.004 | 2.209 | |
get_result-ReactomeAnalysisResult-method | 0.185 | 0.012 | 0.197 | |
get_result | 0.200 | 0.008 | 0.207 | |
load_public_dataset | 1.226 | 0.037 | 4.759 | |
names-ReactomeAnalysisResult-method | 0.178 | 0.004 | 0.182 | |
open_reactome-ReactomeAnalysisResult-method | 0.184 | 0.004 | 0.188 | |
open_reactome | 0.188 | 0.013 | 0.202 | |
pathways-ReactomeAnalysisResult-method | 1.459 | 0.019 | 1.478 | |
pathways | 1.371 | 0.012 | 1.384 | |
perform_reactome_analysis | 3.068 | 0.039 | 16.551 | |
plot_correlations-ReactomeAnalysisResult-method | 1.745 | 0.064 | 1.809 | |
plot_correlations | 1.253 | 0.004 | 1.256 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 33.833 | 0.544 | 75.450 | |
plot_gsva_heatmap | 33.783 | 0.548 | 76.056 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 32.139 | 0.762 | 73.495 | |
plot_gsva_pathway | 32.513 | 0.879 | 74.492 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 31.376 | 0.651 | 72.902 | |
plot_gsva_pca | 32.321 | 0.570 | 74.493 | |
plot_heatmap-ReactomeAnalysisResult-method | 1.501 | 0.024 | 1.525 | |
plot_heatmap | 1.623 | 0.008 | 1.632 | |
plot_volcano-ReactomeAnalysisResult-method | 0.169 | 0.008 | 0.177 | |
plot_volcano | 0.216 | 0.000 | 0.215 | |
print-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.171 | 0.000 | 0.171 | |
reactome_links-ReactomeAnalysisResult-method | 0.165 | 0.004 | 0.169 | |
reactome_links | 0.183 | 0.000 | 0.184 | |
result_types-ReactomeAnalysisResult-method | 0.167 | 0.004 | 0.170 | |
result_types | 0.163 | 0.004 | 0.168 | |
set_method-ReactomeAnalysisRequest-method | 0.000 | 0.002 | 0.002 | |
set_method | 0.000 | 0.002 | 0.002 | |
set_parameters-ReactomeAnalysisRequest-method | 0.000 | 0.001 | 0.001 | |
set_parameters | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.164 | 0.007 | 0.172 | |