| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:37:11 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1693/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.16.1 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 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: 1.16.1 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ReactomeGSA_1.16.1.tar.gz |
| StartedAt: 2024-04-16 04:11:19 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 04:24:34 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 795.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ReactomeGSA_1.16.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* 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 '1.16.1'
* 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 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 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-Seurat-method 35.50 2.40 84.23
plot_gsva_heatmap-ReactomeAnalysisResult-method 35.56 1.01 80.03
analyse_sc_clusters 32.76 1.53 77.91
analyse_sc_clusters-SingleCellExperiment-method 31.40 2.16 82.55
plot_gsva_pca 32.44 0.81 77.39
plot_gsva_heatmap 31.96 1.02 79.17
plot_gsva_pathway 31.23 1.00 75.88
plot_gsva_pca-ReactomeAnalysisResult-method 31.00 1.03 61.50
plot_gsva_pathway-ReactomeAnalysisResult-method 29.45 1.22 78.70
ReactomeAnalysisRequest 5.47 0.52 7.97
perform_reactome_analysis 2.44 0.13 16.82
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'F:/biocbuild/bbs-3.18-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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" 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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
1.15 0.15 1.29
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 5.47 | 0.52 | 7.97 | |
| ReactomeAnalysisResult-class | 1.80 | 0.05 | 1.86 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.74 | 0.00 | 0.74 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 0.67 | 0.04 | 0.72 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.86 | 0.04 | 0.89 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.93 | 0.00 | 0.93 | |
| add_dataset-ReactomeAnalysisRequest-matrix-method | 0.93 | 0.01 | 0.95 | |
| add_dataset | 0.96 | 0.00 | 0.95 | |
| analyse_sc_clusters-Seurat-method | 35.50 | 2.40 | 84.23 | |
| analyse_sc_clusters-SingleCellExperiment-method | 31.40 | 2.16 | 82.55 | |
| analyse_sc_clusters | 32.76 | 1.53 | 77.91 | |
| get_reactome_data_types | 0.00 | 0.02 | 0.53 | |
| get_reactome_methods | 0.02 | 0.06 | 1.53 | |
| get_result-ReactomeAnalysisResult-method | 0.26 | 0.00 | 0.27 | |
| get_result | 0.23 | 0.03 | 0.27 | |
| names-ReactomeAnalysisResult-method | 0.17 | 0.05 | 0.22 | |
| open_reactome-ReactomeAnalysisResult-method | 0.16 | 0.03 | 0.18 | |
| open_reactome | 0.14 | 0.03 | 0.17 | |
| pathways-ReactomeAnalysisResult-method | 1.15 | 0.03 | 1.19 | |
| pathways | 1.23 | 0.03 | 1.27 | |
| perform_reactome_analysis | 2.44 | 0.13 | 16.82 | |
| plot_correlations-ReactomeAnalysisResult-method | 2.04 | 0.07 | 2.13 | |
| plot_correlations | 1.71 | 0.04 | 1.73 | |
| plot_gsva_heatmap-ReactomeAnalysisResult-method | 35.56 | 1.01 | 80.03 | |
| plot_gsva_heatmap | 31.96 | 1.02 | 79.17 | |
| plot_gsva_pathway-ReactomeAnalysisResult-method | 29.45 | 1.22 | 78.70 | |
| plot_gsva_pathway | 31.23 | 1.00 | 75.88 | |
| plot_gsva_pca-ReactomeAnalysisResult-method | 31.00 | 1.03 | 61.50 | |
| plot_gsva_pca | 32.44 | 0.81 | 77.39 | |
| plot_heatmap-ReactomeAnalysisResult-method | 1.92 | 0.06 | 1.98 | |
| plot_heatmap | 1.74 | 0.03 | 1.77 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.19 | 0.00 | 0.19 | |
| plot_volcano | 0.2 | 0.0 | 0.2 | |
| print-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| print-ReactomeAnalysisResult-method | 0.17 | 0.01 | 0.18 | |
| reactome_links-ReactomeAnalysisResult-method | 0.17 | 0.00 | 0.18 | |
| reactome_links | 0.27 | 0.02 | 0.28 | |
| result_types-ReactomeAnalysisResult-method | 0.29 | 0.02 | 0.31 | |
| result_types | 0.19 | 0.00 | 0.19 | |
| set_method-ReactomeAnalysisRequest-method | 0.02 | 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 | 0.22 | 0.03 | 0.25 | |