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This page was generated on 2024-05-04 11:37:03 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ReactomeGSA on nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReactomeGSA_1.18.0.tar.gz
StartedAt: 2024-05-04 02:48:55 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 03:06:27 -0400 (Sat, 04 May 2024)
EllapsedTime: 1051.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ReactomeGSA.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ReactomeGSA_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
analyse_sc_clusters-Seurat-method               33.331  0.804  80.174
plot_gsva_pathway                               33.141  0.524  76.119
plot_gsva_heatmap                               32.375  0.605  73.640
plot_gsva_pathway-ReactomeAnalysisResult-method 32.522  0.364  80.295
analyse_sc_clusters-SingleCellExperiment-method 31.552  0.989  73.326
plot_gsva_heatmap-ReactomeAnalysisResult-method 31.848  0.478  75.792
analyse_sc_clusters                             31.562  0.719  77.900
plot_gsva_pca                                   30.900  0.406  74.065
plot_gsva_pca-ReactomeAnalysisResult-method     30.620  0.519  72.357
ReactomeAnalysisRequest                          4.780  0.300   5.082
load_public_dataset                              3.563  0.103  32.554
perform_reactome_analysis                        3.525  0.104  18.662
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ReactomeGSA.Rcheck/00check.log’
for details.


Installation output

ReactomeGSA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  1.679   0.092   1.759 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest4.7800.3005.082
ReactomeAnalysisResult-class1.2620.0081.271
add_dataset-ReactomeAnalysisRequest-DGEList-method0.7380.0600.798
add_dataset-ReactomeAnalysisRequest-EList-method0.6710.0080.679
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.6580.0040.662
add_dataset-ReactomeAnalysisRequest-data.frame-method0.9680.0200.988
add_dataset-ReactomeAnalysisRequest-matrix-method0.6190.0040.623
add_dataset0.6370.0040.642
analyse_sc_clusters-Seurat-method33.331 0.80480.174
analyse_sc_clusters-SingleCellExperiment-method31.552 0.98973.326
analyse_sc_clusters31.562 0.71977.900
find_public_datasets0.5180.0103.944
get_public_species0.1570.0000.691
get_reactome_data_types0.3300.0081.629
get_reactome_methods0.3570.0042.364
get_result-ReactomeAnalysisResult-method0.1900.0160.206
get_result0.2120.0000.211
load_public_dataset 3.563 0.10332.554
names-ReactomeAnalysisResult-method0.1760.0080.185
open_reactome-ReactomeAnalysisResult-method0.1750.0000.175
open_reactome0.2070.0200.227
pathways-ReactomeAnalysisResult-method1.3160.0161.333
pathways1.2820.0121.295
perform_reactome_analysis 3.525 0.10418.662
plot_correlations-ReactomeAnalysisResult-method1.2470.0081.255
plot_correlations1.2370.0001.237
plot_gsva_heatmap-ReactomeAnalysisResult-method31.848 0.47875.792
plot_gsva_heatmap32.375 0.60573.640
plot_gsva_pathway-ReactomeAnalysisResult-method32.522 0.36480.295
plot_gsva_pathway33.141 0.52476.119
plot_gsva_pca-ReactomeAnalysisResult-method30.620 0.51972.357
plot_gsva_pca30.900 0.40674.065
plot_heatmap-ReactomeAnalysisResult-method1.5200.0481.569
plot_heatmap1.6380.0041.642
plot_volcano-ReactomeAnalysisResult-method0.1810.0040.185
plot_volcano0.1960.0040.200
print-ReactomeAnalysisRequest-method0.0020.0000.002
print-ReactomeAnalysisResult-method0.1700.0040.174
reactome_links-ReactomeAnalysisResult-method0.1870.0000.187
reactome_links0.1660.0080.174
result_types-ReactomeAnalysisResult-method0.1750.0040.179
result_types0.2040.0000.204
set_method-ReactomeAnalysisRequest-method0.0000.0030.002
set_method0.0000.0010.002
set_parameters-ReactomeAnalysisRequest-method0.0010.0000.001
set_parameters0.0010.0000.001
show-ReactomeAnalysisRequest-method0.0010.0000.001
show-ReactomeAnalysisResult-method0.1750.0120.187