Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:40 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 1671/2248 | 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 | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ReactomeGSA_1.19.0.tar.gz |
StartedAt: 2024-07-24 03:13:04 -0400 (Wed, 24 Jul 2024) |
EndedAt: 2024-07-24 03:27:51 -0400 (Wed, 24 Jul 2024) |
EllapsedTime: 886.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ReactomeGSA_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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_heatmap 39.31 2.88 89.60 analyse_sc_clusters-Seurat-method 38.00 2.79 88.99 plot_gsva_pca 37.65 3.10 85.75 plot_gsva_heatmap-ReactomeAnalysisResult-method 38.20 2.51 86.04 analyse_sc_clusters-SingleCellExperiment-method 37.34 2.75 87.45 plot_gsva_pathway-ReactomeAnalysisResult-method 35.77 3.06 83.31 plot_gsva_pathway 35.65 3.06 85.95 analyse_sc_clusters 34.61 3.04 81.79 plot_gsva_pca-ReactomeAnalysisResult-method 31.82 2.22 43.97 ReactomeAnalysisRequest 6.02 0.54 10.21 perform_reactome_analysis 2.50 0.45 46.27 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck/00check.log' for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 1.71 0.21 2.00
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.02 | 0.54 | 10.21 | |
ReactomeAnalysisResult-class | 1.59 | 0.00 | 1.61 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.91 | 0.01 | 0.92 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.79 | 0.03 | 0.83 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 1.22 | 0.05 | 1.28 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.96 | 0.06 | 1.01 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.79 | 0.14 | 0.94 | |
add_dataset | 0.83 | 0.11 | 0.94 | |
analyse_sc_clusters-Seurat-method | 38.00 | 2.79 | 88.99 | |
analyse_sc_clusters-SingleCellExperiment-method | 37.34 | 2.75 | 87.45 | |
analyse_sc_clusters | 34.61 | 3.04 | 81.79 | |
find_public_datasets | 0.05 | 0.02 | 1.84 | |
get_public_species | 0.0 | 0.0 | 0.3 | |
get_reactome_data_types | 0.01 | 0.01 | 0.69 | |
get_reactome_methods | 0.03 | 0.03 | 1.26 | |
get_result-ReactomeAnalysisResult-method | 0.22 | 0.02 | 0.24 | |
get_result | 0.24 | 0.05 | 0.28 | |
load_public_dataset | 1.92 | 0.11 | 4.71 | |
names-ReactomeAnalysisResult-method | 0.16 | 0.06 | 0.24 | |
open_reactome-ReactomeAnalysisResult-method | 0.18 | 0.00 | 0.19 | |
open_reactome | 0.19 | 0.00 | 0.19 | |
pathways-ReactomeAnalysisResult-method | 1.92 | 0.13 | 2.05 | |
pathways | 1.65 | 0.03 | 1.68 | |
perform_reactome_analysis | 2.50 | 0.45 | 46.27 | |
plot_correlations-ReactomeAnalysisResult-method | 1.71 | 0.10 | 1.80 | |
plot_correlations | 1.72 | 0.03 | 1.75 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 38.20 | 2.51 | 86.04 | |
plot_gsva_heatmap | 39.31 | 2.88 | 89.60 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 35.77 | 3.06 | 83.31 | |
plot_gsva_pathway | 35.65 | 3.06 | 85.95 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 31.82 | 2.22 | 43.97 | |
plot_gsva_pca | 37.65 | 3.10 | 85.75 | |
plot_heatmap-ReactomeAnalysisResult-method | 2.22 | 0.09 | 2.31 | |
plot_heatmap | 2.11 | 0.03 | 2.14 | |
plot_volcano-ReactomeAnalysisResult-method | 0.25 | 0.05 | 0.30 | |
plot_volcano | 0.28 | 0.05 | 0.33 | |
print-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
print-ReactomeAnalysisResult-method | 0.24 | 0.00 | 0.25 | |
reactome_links-ReactomeAnalysisResult-method | 0.21 | 0.02 | 0.23 | |
reactome_links | 0.19 | 0.01 | 0.20 | |
result_types-ReactomeAnalysisResult-method | 0.17 | 0.05 | 0.22 | |
result_types | 0.24 | 0.02 | 0.25 | |
set_method-ReactomeAnalysisRequest-method | 0.01 | 0.01 | 0.03 | |
set_method | 0 | 0 | 0 | |
set_parameters-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
set_parameters | 0 | 0 | 0 | |
show-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
show-ReactomeAnalysisResult-method | 0.23 | 0.03 | 0.26 | |