Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:35:41 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 1663/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.14.0 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / 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: 1.14.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ReactomeGSA_1.14.0.tar.gz |
StartedAt: 2023-10-16 00:17:34 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 00:33:37 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 962.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ReactomeGSA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ReactomeGSA_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ReactomeGSA.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.14.0’ * 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 R 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 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 analyse_sc_clusters-SingleCellExperiment-method 39.543 1.340 109.514 plot_gsva_heatmap-ReactomeAnalysisResult-method 39.953 0.912 102.286 plot_gsva_pca 38.463 0.483 104.128 plot_gsva_heatmap 38.167 0.707 93.775 analyse_sc_clusters-Seurat-method 37.381 1.366 97.264 analyse_sc_clusters 37.234 1.042 91.992 plot_gsva_pathway 37.775 0.486 97.681 plot_gsva_pathway-ReactomeAnalysisResult-method 37.439 0.677 91.273 plot_gsva_pca-ReactomeAnalysisResult-method 36.941 0.556 92.422 perform_reactome_analysis 3.717 0.093 19.602 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘analysing-scRNAseq.Rmd’ using ‘UTF-8’... OK ‘using-reactomegsa.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘analysing-scRNAseq.Rmd’ using rmarkdown Quitting from lines 38-47 [unnamed-chunk-1] (analysing-scRNAseq.Rmd) Error: processing vignette 'analysing-scRNAseq.Rmd' failed with diagnostics: trying to use CRAN without setting a mirror --- failed re-building ‘analysing-scRNAseq.Rmd’ --- re-building ‘using-reactomegsa.Rmd’ using rmarkdown Quitting from lines 42-47 [unnamed-chunk-1] (using-reactomegsa.Rmd) Error: processing vignette 'using-reactomegsa.Rmd' failed with diagnostics: trying to use CRAN without setting a mirror --- failed re-building ‘using-reactomegsa.Rmd’ SUMMARY: processing the following files failed: ‘analysing-scRNAseq.Rmd’ ‘using-reactomegsa.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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” in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="ExpressionSet"’: no definition for class “ExpressionSet” ** 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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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 1.057 0.105 1.152
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.024 | 0.276 | 4.302 | |
ReactomeAnalysisResult-class | 1.260 | 0.052 | 1.313 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.658 | 0.004 | 0.661 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.585 | 0.008 | 0.593 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.603 | 0.016 | 0.619 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.602 | 0.000 | 0.602 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.913 | 0.024 | 0.936 | |
add_dataset | 0.570 | 0.004 | 0.573 | |
analyse_sc_clusters-Seurat-method | 37.381 | 1.366 | 97.264 | |
analyse_sc_clusters-SingleCellExperiment-method | 39.543 | 1.340 | 109.514 | |
analyse_sc_clusters | 37.234 | 1.042 | 91.992 | |
get_reactome_data_types | 0.403 | 0.000 | 1.556 | |
get_reactome_methods | 0.498 | 0.008 | 2.790 | |
get_result-ReactomeAnalysisResult-method | 0.181 | 0.004 | 0.185 | |
get_result | 0.176 | 0.000 | 0.175 | |
names-ReactomeAnalysisResult-method | 0.169 | 0.004 | 0.174 | |
open_reactome-ReactomeAnalysisResult-method | 0.152 | 0.012 | 0.164 | |
open_reactome | 0.158 | 0.004 | 0.163 | |
pathways-ReactomeAnalysisResult-method | 1.327 | 0.012 | 1.339 | |
pathways | 1.698 | 0.108 | 1.807 | |
perform_reactome_analysis | 3.717 | 0.093 | 19.602 | |
plot_correlations-ReactomeAnalysisResult-method | 1.335 | 0.004 | 1.339 | |
plot_correlations | 1.326 | 0.000 | 1.326 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 39.953 | 0.912 | 102.286 | |
plot_gsva_heatmap | 38.167 | 0.707 | 93.775 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 37.439 | 0.677 | 91.273 | |
plot_gsva_pathway | 37.775 | 0.486 | 97.681 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 36.941 | 0.556 | 92.422 | |
plot_gsva_pca | 38.463 | 0.483 | 104.128 | |
plot_heatmap-ReactomeAnalysisResult-method | 1.648 | 0.052 | 1.700 | |
plot_heatmap | 1.589 | 0.008 | 1.597 | |
plot_volcano-ReactomeAnalysisResult-method | 0.179 | 0.000 | 0.179 | |
plot_volcano | 0.208 | 0.000 | 0.208 | |
print-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.159 | 0.012 | 0.172 | |
reactome_links-ReactomeAnalysisResult-method | 0.169 | 0.000 | 0.169 | |
reactome_links | 0.194 | 0.006 | 0.200 | |
result_types-ReactomeAnalysisResult-method | 0.179 | 0.004 | 0.183 | |
result_types | 0.168 | 0.000 | 0.168 | |
set_method-ReactomeAnalysisRequest-method | 0.001 | 0.001 | 0.003 | |
set_method | 0.000 | 0.002 | 0.002 | |
set_parameters-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
set_parameters | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.161 | 0.004 | 0.166 | |