Johannes Griss
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/ReactomeGSA |
| git_branch: devel |
| git_last_commit: 1612e12 |
| git_last_commit_date: 2024-11-27 14:03:16 -0500 (Wed, 27 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:38 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| 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 1692/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReactomeGSA 1.21.2 (landing page) Johannes Griss
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.21.2 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ReactomeGSA_1.21.2.tar.gz |
| StartedAt: 2025-01-25 04:59:57 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 05:15:31 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 933.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReactomeGSA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ReactomeGSA_1.21.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '1.21.2'
* 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_pca 39.96 3.03 74.78
plot_gsva_pca-ReactomeAnalysisResult-method 39.63 3.17 74.90
plot_gsva_pathway 39.69 3.02 73.96
plot_gsva_heatmap 39.05 2.75 74.73
plot_gsva_heatmap-ReactomeAnalysisResult-method 38.25 2.60 72.60
analyse_sc_clusters-Seurat-method 38.06 2.22 78.51
analyse_sc_clusters-SingleCellExperiment-method 36.74 2.55 71.97
analyse_sc_clusters 35.67 2.84 112.72
plot_gsva_pathway-ReactomeAnalysisResult-method 35.27 2.65 69.31
generate_pseudo_bulk_data 15.41 2.05 18.29
ReactomeAnalysisRequest 5.61 0.54 7.32
perform_reactome_analysis 2.53 0.25 56.12
load_public_dataset 1.98 0.18 37.62
* 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
'E:/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'ReactomeGSA' ... ** this is package 'ReactomeGSA' version '1.21.2' ** 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 'generate_pseudo_bulk_data' with signature 'object="Seurat"': no definition for class "Seurat" in method for 'generate_pseudo_bulk_data' with signature 'object="SingleCellExperiment"': no definition for class "SingleCellExperiment" ** 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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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
1.70 0.21 2.26
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
| name | user | system | elapsed | |
| ReactomeAnalysisRequest | 5.61 | 0.54 | 7.32 | |
| ReactomeAnalysisResult-class | 0.33 | 0.04 | 0.39 | |
| add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.84 | 0.13 | 0.97 | |
| add_dataset-ReactomeAnalysisRequest-EList-method | 1.36 | 0.06 | 1.42 | |
| add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.70 | 0.13 | 0.83 | |
| add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.97 | 0.06 | 1.03 | |
| add_dataset-ReactomeAnalysisRequest-matrix-method | 0.80 | 0.06 | 0.86 | |
| add_dataset | 0.64 | 0.06 | 0.71 | |
| analyse_sc_clusters-Seurat-method | 38.06 | 2.22 | 78.51 | |
| analyse_sc_clusters-SingleCellExperiment-method | 36.74 | 2.55 | 71.97 | |
| analyse_sc_clusters | 35.67 | 2.84 | 112.72 | |
| find_public_datasets | 0.03 | 0.03 | 3.83 | |
| generate_metadata | 0 | 0 | 0 | |
| generate_pseudo_bulk_data | 15.41 | 2.05 | 18.29 | |
| get_public_species | 0.02 | 0.00 | 0.30 | |
| get_reactome_data_types | 0.01 | 0.02 | 0.59 | |
| get_reactome_methods | 0.05 | 0.00 | 0.92 | |
| get_result-ReactomeAnalysisResult-method | 0.23 | 0.04 | 0.28 | |
| get_result | 0.27 | 0.03 | 0.30 | |
| load_public_dataset | 1.98 | 0.18 | 37.62 | |
| names-ReactomeAnalysisResult-method | 0.22 | 0.04 | 0.27 | |
| open_reactome-ReactomeAnalysisResult-method | 0.23 | 0.03 | 0.26 | |
| open_reactome | 0.28 | 0.00 | 0.28 | |
| pathways-ReactomeAnalysisResult-method | 0.28 | 0.04 | 0.31 | |
| pathways | 0.30 | 0.03 | 0.33 | |
| perform_reactome_analysis | 2.53 | 0.25 | 56.12 | |
| plot_correlations-ReactomeAnalysisResult-method | 0.27 | 0.03 | 0.30 | |
| plot_correlations | 0.23 | 0.04 | 0.28 | |
| plot_gsva_heatmap-ReactomeAnalysisResult-method | 38.25 | 2.60 | 72.60 | |
| plot_gsva_heatmap | 39.05 | 2.75 | 74.73 | |
| plot_gsva_pathway-ReactomeAnalysisResult-method | 35.27 | 2.65 | 69.31 | |
| plot_gsva_pathway | 39.69 | 3.02 | 73.96 | |
| plot_gsva_pca-ReactomeAnalysisResult-method | 39.63 | 3.17 | 74.90 | |
| plot_gsva_pca | 39.96 | 3.03 | 74.78 | |
| plot_heatmap-ReactomeAnalysisResult-method | 0.55 | 0.08 | 0.63 | |
| plot_heatmap | 0.78 | 0.05 | 0.81 | |
| plot_volcano-ReactomeAnalysisResult-method | 0.21 | 0.03 | 0.24 | |
| plot_volcano | 0.32 | 0.00 | 0.32 | |
| print-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| print-ReactomeAnalysisResult-method | 0.27 | 0.03 | 0.30 | |
| reactome_links-ReactomeAnalysisResult-method | 0.23 | 0.02 | 0.25 | |
| reactome_links | 0.27 | 0.03 | 0.30 | |
| result_types-ReactomeAnalysisResult-method | 0.20 | 0.01 | 0.22 | |
| result_types | 0.20 | 0.03 | 0.24 | |
| set_method-ReactomeAnalysisRequest-method | 0.02 | 0.00 | 0.03 | |
| set_method | 0 | 0 | 0 | |
| set_parameters-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| set_parameters | 0.00 | 0.02 | 0.01 | |
| show-ReactomeAnalysisRequest-method | 0 | 0 | 0 | |
| show-ReactomeAnalysisResult-method | 0.28 | 0.03 | 0.32 | |