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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1685/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.21.2  (landing page)
Johannes Griss
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
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)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


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: 1.21.2
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_1.21.2.tar.gz
StartedAt: 2024-12-23 20:56:38 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 21:05:17 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 518.5 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_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ReactomeGSA.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* 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 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-ReactomeAnalysisResult-method 10.764  0.788  43.217
plot_gsva_pathway                               10.409  0.970  43.994
plot_gsva_pca-ReactomeAnalysisResult-method     10.347  1.021  44.635
plot_gsva_heatmap                               10.046  0.969  43.075
plot_gsva_pca                                   10.028  0.984  42.350
plot_gsva_pathway-ReactomeAnalysisResult-method  9.872  1.014  42.980
analyse_sc_clusters-Seurat-method               10.080  0.742  43.249
analyse_sc_clusters                              9.863  0.922  81.364
analyse_sc_clusters-SingleCellExperiment-method  9.795  0.818  43.317
generate_pseudo_bulk_data                        5.658  0.455   6.126
perform_reactome_analysis                        1.405  0.086  14.988
load_public_dataset                              0.608  0.085  32.028
* 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-3.21-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/4.5-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”
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)

Tests output

ReactomeGSA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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 
  0.587   0.057   0.648 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest1.8520.1151.979
ReactomeAnalysisResult-class0.0810.0040.085
add_dataset-ReactomeAnalysisRequest-DGEList-method0.3230.0300.354
add_dataset-ReactomeAnalysisRequest-EList-method0.2730.0270.300
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.2660.0310.298
add_dataset-ReactomeAnalysisRequest-data.frame-method0.4280.0280.455
add_dataset-ReactomeAnalysisRequest-matrix-method0.2580.0310.288
add_dataset0.2550.0320.291
analyse_sc_clusters-Seurat-method10.080 0.74243.249
analyse_sc_clusters-SingleCellExperiment-method 9.795 0.81843.317
analyse_sc_clusters 9.863 0.92281.364
find_public_datasets0.0370.0072.772
generate_metadata0.0010.0000.001
generate_pseudo_bulk_data5.6580.4556.126
get_public_species0.0100.0040.286
get_reactome_data_types0.0220.0040.569
get_reactome_methods0.0340.0091.166
get_result-ReactomeAnalysisResult-method0.0840.0040.088
get_result0.0840.0030.088
load_public_dataset 0.608 0.08532.028
names-ReactomeAnalysisResult-method0.0880.0040.092
open_reactome-ReactomeAnalysisResult-method0.0880.0030.091
open_reactome0.0850.0040.090
pathways-ReactomeAnalysisResult-method0.1070.0040.136
pathways0.0900.0030.094
perform_reactome_analysis 1.405 0.08614.988
plot_correlations-ReactomeAnalysisResult-method0.1120.0060.117
plot_correlations0.1020.0060.108
plot_gsva_heatmap-ReactomeAnalysisResult-method10.764 0.78843.217
plot_gsva_heatmap10.046 0.96943.075
plot_gsva_pathway-ReactomeAnalysisResult-method 9.872 1.01442.980
plot_gsva_pathway10.409 0.97043.994
plot_gsva_pca-ReactomeAnalysisResult-method10.347 1.02144.635
plot_gsva_pca10.028 0.98442.350
plot_heatmap-ReactomeAnalysisResult-method0.1680.0050.173
plot_heatmap0.2000.0050.207
plot_volcano-ReactomeAnalysisResult-method0.1000.0040.105
plot_volcano0.0940.0030.101
print-ReactomeAnalysisRequest-method0.0000.0000.001
print-ReactomeAnalysisResult-method0.0860.0030.090
reactome_links-ReactomeAnalysisResult-method0.0910.0030.096
reactome_links0.0920.0030.095
result_types-ReactomeAnalysisResult-method0.0900.0030.100
result_types0.0880.0030.092
set_method-ReactomeAnalysisRequest-method0.0010.0010.002
set_method0.0000.0010.002
set_parameters-ReactomeAnalysisRequest-method0.0010.0000.001
set_parameters000
show-ReactomeAnalysisRequest-method000
show-ReactomeAnalysisResult-method0.0890.0040.093