Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:37 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the ReactomeGSA package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1558/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.8.0 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ReactomeGSA |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReactomeGSA_1.8.0.tar.gz |
StartedAt: 2022-04-12 17:24:39 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 17:41:58 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 1038.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReactomeGSA_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.8.0’ * 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 R 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 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 66.006 2.314 105.360 plot_gsva_heatmap-ReactomeAnalysisResult-method 65.011 1.984 108.873 analyse_sc_clusters-SingleCellExperiment-method 63.866 2.122 100.374 analyse_sc_clusters 63.787 2.008 104.896 plot_gsva_heatmap 63.522 1.696 98.473 plot_gsva_pathway-ReactomeAnalysisResult-method 61.554 1.984 104.003 plot_gsva_pathway 60.820 1.703 101.619 plot_gsva_pca 59.971 2.194 94.621 plot_gsva_pca-ReactomeAnalysisResult-method 58.647 1.857 99.250 ReactomeAnalysisRequest 6.092 0.366 6.470 perform_reactome_analysis 3.227 0.165 14.262 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.14-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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” in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="ExpressionSet"’: no definition for class “ExpressionSet” ** 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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 2.052 0.183 2.217
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.092 | 0.366 | 6.470 | |
ReactomeAnalysisResult-class | 2.868 | 0.012 | 2.882 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.190 | 0.083 | 1.274 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 1.138 | 0.057 | 1.195 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.990 | 0.047 | 1.038 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.314 | 0.046 | 1.360 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 1.089 | 0.065 | 1.155 | |
add_dataset | 1.057 | 0.050 | 1.109 | |
analyse_sc_clusters-Seurat-method | 66.006 | 2.314 | 105.360 | |
analyse_sc_clusters-SingleCellExperiment-method | 63.866 | 2.122 | 100.374 | |
analyse_sc_clusters | 63.787 | 2.008 | 104.896 | |
get_reactome_data_types | 0.095 | 0.007 | 1.764 | |
get_reactome_methods | 0.157 | 0.014 | 2.671 | |
get_result-ReactomeAnalysisResult-method | 0.280 | 0.009 | 0.288 | |
get_result | 0.257 | 0.008 | 0.265 | |
names-ReactomeAnalysisResult-method | 0.268 | 0.008 | 0.275 | |
open_reactome-ReactomeAnalysisResult-method | 0.250 | 0.007 | 0.258 | |
open_reactome | 0.268 | 0.007 | 0.276 | |
pathways-ReactomeAnalysisResult-method | 3.482 | 0.100 | 3.584 | |
pathways | 2.538 | 0.010 | 2.548 | |
perform_reactome_analysis | 3.227 | 0.165 | 14.262 | |
plot_correlations-ReactomeAnalysisResult-method | 2.506 | 0.034 | 2.540 | |
plot_correlations | 3.110 | 0.010 | 3.122 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 65.011 | 1.984 | 108.873 | |
plot_gsva_heatmap | 63.522 | 1.696 | 98.473 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 61.554 | 1.984 | 104.003 | |
plot_gsva_pathway | 60.820 | 1.703 | 101.619 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 58.647 | 1.857 | 99.250 | |
plot_gsva_pca | 59.971 | 2.194 | 94.621 | |
plot_heatmap-ReactomeAnalysisResult-method | 2.995 | 0.054 | 3.051 | |
plot_heatmap | 2.935 | 0.010 | 2.947 | |
plot_volcano-ReactomeAnalysisResult-method | 0.253 | 0.006 | 0.260 | |
plot_volcano | 0.252 | 0.006 | 0.259 | |
print-ReactomeAnalysisRequest-method | 0.003 | 0.001 | 0.004 | |
print-ReactomeAnalysisResult-method | 0.240 | 0.007 | 0.247 | |
reactome_links-ReactomeAnalysisResult-method | 0.226 | 0.007 | 0.233 | |
reactome_links | 0.218 | 0.005 | 0.224 | |
result_types-ReactomeAnalysisResult-method | 0.219 | 0.006 | 0.226 | |
result_types | 0.231 | 0.007 | 0.238 | |
set_method-ReactomeAnalysisRequest-method | 0.003 | 0.003 | 0.005 | |
set_method | 0.003 | 0.002 | 0.004 | |
set_parameters-ReactomeAnalysisRequest-method | 0.003 | 0.001 | 0.003 | |
set_parameters | 0.002 | 0.001 | 0.003 | |
show-ReactomeAnalysisRequest-method | 0.002 | 0.001 | 0.003 | |
show-ReactomeAnalysisResult-method | 0.189 | 0.005 | 0.194 | |