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This page was generated on 2024-06-11 14:44 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1713/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.18.0  (landing page)
Johannes Griss
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_19
git_last_commit: 4bfdb0f
git_last_commit_date: 2024-04-30 11:17:23 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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  UNNEEDED, same version is already published


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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2024-06-11 02:34:54 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 02:52:14 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 1039.9 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.18.0’
* 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 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                               36.450  2.051  96.132
analyse_sc_clusters                             36.358  2.033 100.667
plot_gsva_heatmap-ReactomeAnalysisResult-method 36.638  1.655  89.546
plot_gsva_pca-ReactomeAnalysisResult-method     35.917  2.238  94.545
analyse_sc_clusters-Seurat-method               36.029  1.829  95.899
plot_gsva_pathway                               36.127  1.729  92.121
plot_gsva_pathway-ReactomeAnalysisResult-method 35.594  1.904  95.734
plot_gsva_pca                                   35.362  2.025  95.882
analyse_sc_clusters-SingleCellExperiment-method 33.940  1.915  93.929
ReactomeAnalysisRequest                          5.671  0.396   8.569
perform_reactome_analysis                        2.772  0.258  19.088
load_public_dataset                              1.335  0.165  34.259
* 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-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
  1.858   0.196   3.161 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest5.6710.3968.569
ReactomeAnalysisResult-class1.2480.0221.566
add_dataset-ReactomeAnalysisRequest-DGEList-method0.9710.0441.698
add_dataset-ReactomeAnalysisRequest-EList-method0.7590.0470.868
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.7670.0310.799
add_dataset-ReactomeAnalysisRequest-data.frame-method1.3530.0561.720
add_dataset-ReactomeAnalysisRequest-matrix-method0.7100.0591.153
add_dataset0.7050.0561.048
analyse_sc_clusters-Seurat-method36.029 1.82995.899
analyse_sc_clusters-SingleCellExperiment-method33.940 1.91593.929
analyse_sc_clusters 36.358 2.033100.667
find_public_datasets0.0930.0173.631
get_public_species0.0270.0070.759
get_reactome_data_types0.0510.0131.289
get_reactome_methods0.0870.0222.051
get_result-ReactomeAnalysisResult-method0.2420.0110.371
get_result0.2430.0120.442
load_public_dataset 1.335 0.16534.259
names-ReactomeAnalysisResult-method0.2470.0120.363
open_reactome-ReactomeAnalysisResult-method0.2310.0110.247
open_reactome0.2320.0100.243
pathways-ReactomeAnalysisResult-method1.6120.0171.927
pathways1.5350.0272.189
perform_reactome_analysis 2.772 0.25819.088
plot_correlations-ReactomeAnalysisResult-method1.4180.0381.743
plot_correlations1.4100.0212.008
plot_gsva_heatmap-ReactomeAnalysisResult-method36.638 1.65589.546
plot_gsva_heatmap36.450 2.05196.132
plot_gsva_pathway-ReactomeAnalysisResult-method35.594 1.90495.734
plot_gsva_pathway36.127 1.72992.121
plot_gsva_pca-ReactomeAnalysisResult-method35.917 2.23894.545
plot_gsva_pca35.362 2.02595.882
plot_heatmap-ReactomeAnalysisResult-method1.8220.0442.287
plot_heatmap2.0090.0262.808
plot_volcano-ReactomeAnalysisResult-method0.2700.0110.455
plot_volcano0.2970.0140.526
print-ReactomeAnalysisRequest-method0.0020.0000.002
print-ReactomeAnalysisResult-method0.2680.0140.502
reactome_links-ReactomeAnalysisResult-method0.2730.0150.513
reactome_links0.2690.0120.458
result_types-ReactomeAnalysisResult-method0.2330.0100.242
result_types0.2300.0100.241
set_method-ReactomeAnalysisRequest-method0.0020.0020.005
set_method0.0020.0020.008
set_parameters-ReactomeAnalysisRequest-method0.0010.0010.002
set_parameters0.0010.0000.001
show-ReactomeAnalysisRequest-method0.0020.0000.006
show-ReactomeAnalysisResult-method0.2580.0120.479