Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:45 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 1658/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.19.0 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | 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 | see weekly results here | ||||||||||||
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: /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_1.19.0.tar.gz |
StartedAt: 2024-05-02 09:57:35 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 10:24:26 -0400 (Thu, 02 May 2024) |
EllapsedTime: 1611.4 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.19.0’ * 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 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_pca 88.973 1.932 146.380 plot_gsva_heatmap-ReactomeAnalysisResult-method 88.731 1.540 149.282 analyse_sc_clusters-Seurat-method 87.439 2.433 159.196 plot_gsva_pca-ReactomeAnalysisResult-method 86.618 2.008 151.121 plot_gsva_pathway 86.401 1.990 152.039 plot_gsva_heatmap 85.688 2.161 147.084 plot_gsva_pathway-ReactomeAnalysisResult-method 85.137 2.195 156.467 analyse_sc_clusters-SingleCellExperiment-method 84.919 2.259 145.455 analyse_sc_clusters 83.788 2.255 140.677 ReactomeAnalysisRequest 11.772 0.754 15.917 perform_reactome_analysis 5.201 0.306 19.452 plot_heatmap 5.140 0.050 6.043 plot_heatmap-ReactomeAnalysisResult-method 4.624 0.073 5.574 load_public_dataset 2.478 0.189 33.126 * 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 ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/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” ** 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 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 3.521 0.328 4.500
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 11.772 | 0.754 | 15.917 | |
ReactomeAnalysisResult-class | 3.936 | 0.043 | 4.540 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 1.569 | 0.060 | 1.852 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 1.424 | 0.045 | 1.780 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 1.431 | 0.042 | 1.919 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.801 | 0.049 | 2.420 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 1.363 | 0.049 | 1.856 | |
add_dataset | 1.387 | 0.044 | 1.920 | |
analyse_sc_clusters-Seurat-method | 87.439 | 2.433 | 159.196 | |
analyse_sc_clusters-SingleCellExperiment-method | 84.919 | 2.259 | 145.455 | |
analyse_sc_clusters | 83.788 | 2.255 | 140.677 | |
find_public_datasets | 0.179 | 0.024 | 3.425 | |
get_public_species | 0.043 | 0.006 | 0.845 | |
get_reactome_data_types | 0.088 | 0.012 | 0.683 | |
get_reactome_methods | 0.154 | 0.022 | 1.307 | |
get_result-ReactomeAnalysisResult-method | 0.348 | 0.016 | 0.380 | |
get_result | 0.335 | 0.015 | 0.402 | |
load_public_dataset | 2.478 | 0.189 | 33.126 | |
names-ReactomeAnalysisResult-method | 0.340 | 0.017 | 0.428 | |
open_reactome-ReactomeAnalysisResult-method | 0.347 | 0.015 | 0.436 | |
open_reactome | 0.400 | 0.055 | 0.553 | |
pathways-ReactomeAnalysisResult-method | 4.045 | 0.039 | 4.882 | |
pathways | 3.974 | 0.040 | 4.843 | |
perform_reactome_analysis | 5.201 | 0.306 | 19.452 | |
plot_correlations-ReactomeAnalysisResult-method | 3.954 | 0.061 | 4.796 | |
plot_correlations | 3.901 | 0.042 | 4.637 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 88.731 | 1.540 | 149.282 | |
plot_gsva_heatmap | 85.688 | 2.161 | 147.084 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 85.137 | 2.195 | 156.467 | |
plot_gsva_pathway | 86.401 | 1.990 | 152.039 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 86.618 | 2.008 | 151.121 | |
plot_gsva_pca | 88.973 | 1.932 | 146.380 | |
plot_heatmap-ReactomeAnalysisResult-method | 4.624 | 0.073 | 5.574 | |
plot_heatmap | 5.140 | 0.050 | 6.043 | |
plot_volcano-ReactomeAnalysisResult-method | 0.388 | 0.015 | 0.459 | |
plot_volcano | 0.427 | 0.015 | 0.513 | |
print-ReactomeAnalysisRequest-method | 0.003 | 0.002 | 0.004 | |
print-ReactomeAnalysisResult-method | 0.342 | 0.015 | 0.413 | |
reactome_links-ReactomeAnalysisResult-method | 0.334 | 0.016 | 0.410 | |
reactome_links | 0.326 | 0.014 | 0.401 | |
result_types-ReactomeAnalysisResult-method | 0.337 | 0.016 | 0.408 | |
result_types | 0.334 | 0.015 | 0.411 | |
set_method-ReactomeAnalysisRequest-method | 0.004 | 0.003 | 0.007 | |
set_method | 0.003 | 0.002 | 0.007 | |
set_parameters-ReactomeAnalysisRequest-method | 0.003 | 0.001 | 0.004 | |
set_parameters | 0.003 | 0.000 | 0.005 | |
show-ReactomeAnalysisRequest-method | 0.003 | 0.001 | 0.004 | |
show-ReactomeAnalysisResult-method | 0.334 | 0.016 | 0.411 | |