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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1698/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.20.0  (landing page)
Johannes Griss
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_20
git_last_commit: b1f2efd
git_last_commit_date: 2024-10-29 10:40:10 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ReactomeGSA on kjohnson3

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.

raw results


Summary

Package: ReactomeGSA
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-11-09 10:57:24 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 11:08:49 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 684.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                 user system elapsed
plot_gsva_heatmap                               9.308  0.858  41.629
plot_gsva_heatmap-ReactomeAnalysisResult-method 9.247  0.789  42.254
plot_gsva_pathway                               9.266  0.634  41.467
plot_gsva_pca                                   9.040  0.799  43.540
plot_gsva_pca-ReactomeAnalysisResult-method     9.071  0.687  41.627
plot_gsva_pathway-ReactomeAnalysisResult-method 8.891  0.738  43.610
analyse_sc_clusters-Seurat-method               8.832  0.539  46.999
analyse_sc_clusters                             8.396  0.701  41.350
analyse_sc_clusters-SingleCellExperiment-method 8.497  0.558  41.427
perform_reactome_analysis                       0.860  0.087  14.263
load_public_dataset                             0.648  0.069  34.977
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

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-arm64/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)

Tests output

ReactomeGSA.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
  0.522   0.039   0.560 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest1.5360.0741.639
ReactomeAnalysisResult-class0.3770.0030.379
add_dataset-ReactomeAnalysisRequest-DGEList-method0.2560.0120.269
add_dataset-ReactomeAnalysisRequest-EList-method0.2210.0230.244
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.2220.0210.242
add_dataset-ReactomeAnalysisRequest-data.frame-method0.3350.0310.367
add_dataset-ReactomeAnalysisRequest-matrix-method0.2140.0300.244
add_dataset0.2130.0260.239
analyse_sc_clusters-Seurat-method 8.832 0.53946.999
analyse_sc_clusters-SingleCellExperiment-method 8.497 0.55841.427
analyse_sc_clusters 8.396 0.70141.350
find_public_datasets0.0320.0062.324
get_public_species0.0090.0010.264
get_reactome_data_types0.0170.0030.555
get_reactome_methods0.0290.0040.847
get_result-ReactomeAnalysisResult-method0.0680.0020.070
get_result0.0650.0020.067
load_public_dataset 0.648 0.06934.977
names-ReactomeAnalysisResult-method0.0690.0020.072
open_reactome-ReactomeAnalysisResult-method0.0690.0030.071
open_reactome0.0680.0040.072
pathways-ReactomeAnalysisResult-method0.4680.0040.472
pathways0.4920.0150.507
perform_reactome_analysis 0.860 0.08714.263
plot_correlations-ReactomeAnalysisResult-method0.460.010.47
plot_correlations0.4520.0030.455
plot_gsva_heatmap-ReactomeAnalysisResult-method 9.247 0.78942.254
plot_gsva_heatmap 9.308 0.85841.629
plot_gsva_pathway-ReactomeAnalysisResult-method 8.891 0.73843.610
plot_gsva_pathway 9.266 0.63441.467
plot_gsva_pca-ReactomeAnalysisResult-method 9.071 0.68741.627
plot_gsva_pca 9.040 0.79943.540
plot_heatmap-ReactomeAnalysisResult-method0.5080.0100.518
plot_heatmap0.5710.0110.582
plot_volcano-ReactomeAnalysisResult-method0.0770.0030.080
plot_volcano0.0920.0030.094
print-ReactomeAnalysisRequest-method0.0000.0000.001
print-ReactomeAnalysisResult-method0.0780.0030.080
reactome_links-ReactomeAnalysisResult-method0.0740.0020.075
reactome_links0.0740.0020.076
result_types-ReactomeAnalysisResult-method0.0730.0030.075
result_types0.0640.0020.066
set_method-ReactomeAnalysisRequest-method0.0010.0010.001
set_method0.0000.0000.001
set_parameters-ReactomeAnalysisRequest-method0.0010.0000.000
set_parameters0.0000.0000.001
show-ReactomeAnalysisRequest-method0.0010.0000.000
show-ReactomeAnalysisResult-method0.0620.0020.064