Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:37 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for ReactomeGSA on machv2


To the developers/maintainers of the ReactomeGSA package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1558/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.8.0  (landing page)
Johannes Griss
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_14
git_last_commit: 51c41bd
git_last_commit_date: 2021-10-26 12:54:15 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ReactomeGSA
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2022-04-12 17:24:39 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:41:58 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1038.7 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_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReactomeGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReactomeGSA’ version ‘1.8.0’
* 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 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               66.006  2.314 105.360
plot_gsva_heatmap-ReactomeAnalysisResult-method 65.011  1.984 108.873
analyse_sc_clusters-SingleCellExperiment-method 63.866  2.122 100.374
analyse_sc_clusters                             63.787  2.008 104.896
plot_gsva_heatmap                               63.522  1.696  98.473
plot_gsva_pathway-ReactomeAnalysisResult-method 61.554  1.984 104.003
plot_gsva_pathway                               60.820  1.703 101.619
plot_gsva_pca                                   59.971  2.194  94.621
plot_gsva_pca-ReactomeAnalysisResult-method     58.647  1.857  99.250
ReactomeAnalysisRequest                          6.092  0.366   6.470
perform_reactome_analysis                        3.227  0.165  14.262
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.



Installation output

ReactomeGSA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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”
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)

Tests output

ReactomeGSA.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  2.052   0.183   2.217 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest6.0920.3666.470
ReactomeAnalysisResult-class2.8680.0122.882
add_dataset-ReactomeAnalysisRequest-DGEList-method1.1900.0831.274
add_dataset-ReactomeAnalysisRequest-EList-method1.1380.0571.195
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.9900.0471.038
add_dataset-ReactomeAnalysisRequest-data.frame-method1.3140.0461.360
add_dataset-ReactomeAnalysisRequest-matrix-method1.0890.0651.155
add_dataset1.0570.0501.109
analyse_sc_clusters-Seurat-method 66.006 2.314105.360
analyse_sc_clusters-SingleCellExperiment-method 63.866 2.122100.374
analyse_sc_clusters 63.787 2.008104.896
get_reactome_data_types0.0950.0071.764
get_reactome_methods0.1570.0142.671
get_result-ReactomeAnalysisResult-method0.2800.0090.288
get_result0.2570.0080.265
names-ReactomeAnalysisResult-method0.2680.0080.275
open_reactome-ReactomeAnalysisResult-method0.2500.0070.258
open_reactome0.2680.0070.276
pathways-ReactomeAnalysisResult-method3.4820.1003.584
pathways2.5380.0102.548
perform_reactome_analysis 3.227 0.16514.262
plot_correlations-ReactomeAnalysisResult-method2.5060.0342.540
plot_correlations3.1100.0103.122
plot_gsva_heatmap-ReactomeAnalysisResult-method 65.011 1.984108.873
plot_gsva_heatmap63.522 1.69698.473
plot_gsva_pathway-ReactomeAnalysisResult-method 61.554 1.984104.003
plot_gsva_pathway 60.820 1.703101.619
plot_gsva_pca-ReactomeAnalysisResult-method58.647 1.85799.250
plot_gsva_pca59.971 2.19494.621
plot_heatmap-ReactomeAnalysisResult-method2.9950.0543.051
plot_heatmap2.9350.0102.947
plot_volcano-ReactomeAnalysisResult-method0.2530.0060.260
plot_volcano0.2520.0060.259
print-ReactomeAnalysisRequest-method0.0030.0010.004
print-ReactomeAnalysisResult-method0.2400.0070.247
reactome_links-ReactomeAnalysisResult-method0.2260.0070.233
reactome_links0.2180.0050.224
result_types-ReactomeAnalysisResult-method0.2190.0060.226
result_types0.2310.0070.238
set_method-ReactomeAnalysisRequest-method0.0030.0030.005
set_method0.0030.0020.004
set_parameters-ReactomeAnalysisRequest-method0.0030.0010.003
set_parameters0.0020.0010.003
show-ReactomeAnalysisRequest-method0.0020.0010.003
show-ReactomeAnalysisResult-method0.1890.0050.194