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This page was generated on 2024-05-20 11:32:18 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 1659/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.19.0 (landing page) Johannes Griss
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the ReactomeGSA package: - 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: 2024-05-19 23:44:45 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 23:57:48 -0400 (Sun, 19 May 2024) |
EllapsedTime: 782.6 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-mac-arm64/meat/ReactomeGSA.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * 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_pathway 30.262 1.962 71.938 analyse_sc_clusters-Seurat-method 29.922 1.905 90.477 plot_gsva_heatmap-ReactomeAnalysisResult-method 29.868 1.812 72.498 plot_gsva_pathway-ReactomeAnalysisResult-method 29.474 2.012 72.820 plot_gsva_heatmap 29.140 2.005 73.414 plot_gsva_pca-ReactomeAnalysisResult-method 28.927 2.035 72.431 plot_gsva_pca 28.918 1.928 73.473 analyse_sc_clusters-SingleCellExperiment-method 28.308 1.984 71.982 analyse_sc_clusters 27.683 1.937 71.262 ReactomeAnalysisRequest 5.605 0.331 5.988 perform_reactome_analysis 2.783 0.265 15.820 load_public_dataset 0.806 0.093 14.096 * 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-mac-arm64/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-arm64/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: aarch64-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 1.790 0.147 1.933
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 5.605 | 0.331 | 5.988 | |
ReactomeAnalysisResult-class | 1.363 | 0.017 | 1.395 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.955 | 0.067 | 1.022 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.844 | 0.055 | 0.900 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.838 | 0.032 | 0.870 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.253 | 0.076 | 1.328 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.815 | 0.065 | 0.880 | |
add_dataset | 0.805 | 0.067 | 0.872 | |
analyse_sc_clusters-Seurat-method | 29.922 | 1.905 | 90.477 | |
analyse_sc_clusters-SingleCellExperiment-method | 28.308 | 1.984 | 71.982 | |
analyse_sc_clusters | 27.683 | 1.937 | 71.262 | |
find_public_datasets | 0.098 | 0.013 | 1.762 | |
get_public_species | 0.027 | 0.003 | 0.111 | |
get_reactome_data_types | 0.044 | 0.010 | 0.566 | |
get_reactome_methods | 0.073 | 0.012 | 0.340 | |
get_result-ReactomeAnalysisResult-method | 0.262 | 0.011 | 0.278 | |
get_result | 0.263 | 0.010 | 0.276 | |
load_public_dataset | 0.806 | 0.093 | 14.096 | |
names-ReactomeAnalysisResult-method | 0.214 | 0.008 | 0.223 | |
open_reactome-ReactomeAnalysisResult-method | 0.234 | 0.008 | 0.243 | |
open_reactome | 0.275 | 0.009 | 0.284 | |
pathways-ReactomeAnalysisResult-method | 1.721 | 0.027 | 1.747 | |
pathways | 0.967 | 0.015 | 0.988 | |
perform_reactome_analysis | 2.783 | 0.265 | 15.820 | |
plot_correlations-ReactomeAnalysisResult-method | 1.450 | 0.031 | 1.482 | |
plot_correlations | 1.434 | 0.011 | 1.445 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 29.868 | 1.812 | 72.498 | |
plot_gsva_heatmap | 29.140 | 2.005 | 73.414 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 29.474 | 2.012 | 72.820 | |
plot_gsva_pathway | 30.262 | 1.962 | 71.938 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 28.927 | 2.035 | 72.431 | |
plot_gsva_pca | 28.918 | 1.928 | 73.473 | |
plot_heatmap-ReactomeAnalysisResult-method | 1.748 | 0.023 | 1.772 | |
plot_heatmap | 1.858 | 0.012 | 1.870 | |
plot_volcano-ReactomeAnalysisResult-method | 0.264 | 0.011 | 0.285 | |
plot_volcano | 0.285 | 0.009 | 0.294 | |
print-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.268 | 0.009 | 0.276 | |
reactome_links-ReactomeAnalysisResult-method | 0.275 | 0.009 | 0.284 | |
reactome_links | 0.280 | 0.009 | 0.288 | |
result_types-ReactomeAnalysisResult-method | 0.256 | 0.009 | 0.265 | |
result_types | 0.262 | 0.008 | 0.270 | |
set_method-ReactomeAnalysisRequest-method | 0.002 | 0.002 | 0.004 | |
set_method | 0.002 | 0.002 | 0.003 | |
set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.002 | |
set_parameters | 0.001 | 0.001 | 0.001 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.258 | 0.012 | 0.270 | |