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 11:35:18 -0400 (Tue, 28 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReactomeGSA_1.18.0.tar.gz |
StartedAt: 2024-05-28 01:42:17 -0400 (Tue, 28 May 2024) |
EndedAt: 2024-05-28 02:22:17 -0400 (Tue, 28 May 2024) |
EllapsedTime: 2400.5 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: ReactomeGSA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReactomeGSA_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 ...
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.791 | 0.276 | 5.069 | |
ReactomeAnalysisResult-class | 1.265 | 0.016 | 1.282 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.807 | 0.040 | 0.846 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.659 | 0.000 | 0.658 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.635 | 0.000 | 0.635 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 1.010 | 0.008 | 1.018 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.631 | 0.028 | 0.658 | |
add_dataset | 0.625 | 0.008 | 0.633 | |
analyse_sc_clusters-Seurat-method | 32.961 | 0.720 | 77.012 | |
analyse_sc_clusters-SingleCellExperiment-method | 31.750 | 0.660 | 74.657 | |
analyse_sc_clusters | 30.038 | 0.580 | 72.392 | |
find_public_datasets | 0.489 | 0.013 | 3.900 | |
get_public_species | 0.169 | 0.008 | 0.712 | |
get_reactome_data_types | 0.290 | 0.000 | 1.307 | |
get_reactome_methods | 0.507 | 0.012 | 1.921 | |
get_result-ReactomeAnalysisResult-method | 0.196 | 0.004 | 0.200 | |
get_result | 0.18 | 0.00 | 0.18 | |
load_public_dataset | 3.867 | 0.084 | 34.969 | |
names-ReactomeAnalysisResult-method | 0.171 | 0.004 | 0.176 | |
open_reactome-ReactomeAnalysisResult-method | 0.189 | 0.000 | 0.190 | |
open_reactome | 0.212 | 0.016 | 0.228 | |
pathways-ReactomeAnalysisResult-method | 1.282 | 0.004 | 1.286 | |
pathways | 1.283 | 0.000 | 1.284 | |
perform_reactome_analysis | 3.451 | 0.080 | 16.082 | |
plot_correlations-ReactomeAnalysisResult-method | 1.239 | 0.000 | 1.239 | |
plot_correlations | 1.232 | 0.002 | 1.234 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 32.607 | 0.422 | 76.628 | |
plot_gsva_heatmap | 32.473 | 0.736 | 74.966 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 32.056 | 0.941 | 73.793 | |
plot_gsva_pathway | 32.492 | 0.716 | 74.129 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 31.300 | 0.740 | 74.846 | |