Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-28 11:35:50 -0400 (Tue, 28 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4752 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4517 |
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 | TIMEOUT | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: 1.18.0 |
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_1.18.0.tar.gz |
StartedAt: 2024-05-27 23:07:09 -0400 (Mon, 27 May 2024) |
EndedAt: 2024-05-27 23:16:12 -0400 (Mon, 27 May 2024) |
EllapsedTime: 542.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ReactomeGSA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.18.0’ * 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 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 ... ERROR Running examples in ‘ReactomeGSA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_gsva_heatmap > ### Title: plot_gsva_heatmap > ### Aliases: plot_gsva_heatmap > > ### ** Examples > > # load the scRNA-seq example data > library(ReactomeGSA.data) Loading required package: limma Loading required package: edgeR Loading required package: Seurat Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following objects are masked from ‘package:base’: intersect, t > data(jerby_b_cells) > > # perform the GSVA analysis > gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE) Converting expression data to string... (This may take a moment) Conversion complete Compressing request data... Reactome Analysis submitted succesfully > > # plot the heatmap > relevant_pathways <- c("R-HSA-983170", "R-HSA-388841", "R-HSA-2132295", + "R-HSA-983705", "R-HSA-5690714") > plot_gsva_heatmap(gsva_result, + pathway_ids = relevant_pathways, # limit to these pathways + margins = c(6,30), # adapt the figure margins in heatmap.2 + dendrogram = "col", # only plot column dendrogram + scale = "row", # scale for each pathway + key = FALSE, # don't display the color key + lwid=c(0.1,4)) # remove the white space on the left Error: C stack usage 7979480 is too close to the limit Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-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 (2024-04-24) -- "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 1.793 0.210 2.002
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 6.202 | 0.461 | 6.755 | |
ReactomeAnalysisResult-class | 1.554 | 0.029 | 1.599 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.993 | 0.061 | 1.064 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.840 | 0.049 | 0.899 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.854 | 0.036 | 0.901 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.195 | 0.054 | 1.265 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.838 | 0.056 | 0.908 | |
add_dataset | 0.825 | 0.049 | 0.883 | |
analyse_sc_clusters-Seurat-method | 39.197 | 1.781 | 85.039 | |
analyse_sc_clusters-SingleCellExperiment-method | 35.858 | 1.739 | 82.561 | |
analyse_sc_clusters | 35.904 | 1.845 | 86.197 | |
find_public_datasets | 0.109 | 0.020 | 2.150 | |
get_public_species | 0.028 | 0.004 | 0.287 | |
get_reactome_data_types | 0.055 | 0.008 | 0.580 | |
get_reactome_methods | 0.097 | 0.015 | 1.388 | |
get_result-ReactomeAnalysisResult-method | 0.250 | 0.013 | 0.266 | |
get_result | 0.266 | 0.015 | 0.286 | |
load_public_dataset | 1.672 | 0.166 | 34.715 | |
names-ReactomeAnalysisResult-method | 0.242 | 0.012 | 0.258 | |
open_reactome-ReactomeAnalysisResult-method | 0.260 | 0.014 | 0.277 | |
open_reactome | 0.289 | 0.058 | 0.353 | |
pathways-ReactomeAnalysisResult-method | 1.547 | 0.029 | 1.591 | |
pathways | 1.588 | 0.029 | 1.634 | |
perform_reactome_analysis | 3.158 | 0.319 | 16.755 | |
plot_correlations-ReactomeAnalysisResult-method | 1.705 | 0.051 | 1.775 | |
plot_correlations | 1.526 | 0.022 | 1.560 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 38.374 | 1.517 | 89.982 | |