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This page was generated on 2023-03-31 11:06:21 -0400 (Fri, 31 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4498
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4278
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4306
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 palomino4


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 1627/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReactomeGSA 1.12.0  (landing page)
Johannes Griss
Snapshot Date: 2023-03-29 14:00:04 -0400 (Wed, 29 Mar 2023)
git_url: https://git.bioconductor.org/packages/ReactomeGSA
git_branch: RELEASE_3_16
git_last_commit: 8ff0616
git_last_commit_date: 2022-11-01 11:20:32 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ReactomeGSA
Version: 1.12.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ReactomeGSA_1.12.0.tar.gz
StartedAt: 2023-03-30 04:54:13 -0400 (Thu, 30 Mar 2023)
EndedAt: 2023-03-30 05:09:30 -0400 (Thu, 30 Mar 2023)
EllapsedTime: 916.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ReactomeGSA.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ReactomeGSA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ReactomeGSA_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ReactomeGSA.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.12.0'
* 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 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 ... WARNING
Codoc mismatches from documentation object 'plot_heatmap,ReactomeAnalysisResult-method':
\S4method{plot_heatmap}{ReactomeAnalysisResult}
  Code: function(x, fdr = 0.01, max_pathways = 30, break_long_names =
                 TRUE, return_data = FALSE)
  Docs: function(x, fdr = 0.05, max_pathways = 30, break_long_names =
                 TRUE, return_data = FALSE)
  Mismatches in argument default values:
    Name: 'fdr' Code: 0.01 Docs: 0.05

* 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               33.81   2.35   97.12
plot_gsva_pathway                               32.89   1.26   91.31
plot_gsva_pathway-ReactomeAnalysisResult-method 31.78   1.46   88.86
analyse_sc_clusters                             31.83   1.31   94.47
analyse_sc_clusters-SingleCellExperiment-method 30.64   2.09   89.72
plot_gsva_heatmap-ReactomeAnalysisResult-method 31.29   0.98   91.59
plot_gsva_heatmap                               30.81   1.28   91.41
plot_gsva_pca-ReactomeAnalysisResult-method     30.94   1.02   94.02
plot_gsva_pca                                   30.31   1.15   87.11
perform_reactome_analysis                        2.15   0.03   16.73
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/ReactomeGSA.Rcheck/00check.log'
for details.



Installation output

ReactomeGSA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ReactomeGSA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   1.21    0.17    1.37 

Example timings

ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings

nameusersystemelapsed
ReactomeAnalysisRequest4.370.234.66
ReactomeAnalysisResult-class1.270.001.31
add_dataset-ReactomeAnalysisRequest-DGEList-method0.720.020.73
add_dataset-ReactomeAnalysisRequest-EList-method1.060.001.07
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method0.690.090.78
add_dataset-ReactomeAnalysisRequest-data.frame-method0.670.100.77
add_dataset-ReactomeAnalysisRequest-matrix-method0.800.080.87
add_dataset0.690.070.77
analyse_sc_clusters-Seurat-method33.81 2.3597.12
analyse_sc_clusters-SingleCellExperiment-method30.64 2.0989.72
analyse_sc_clusters31.83 1.3194.47
get_reactome_data_types0.020.001.57
get_reactome_methods0.000.022.62
get_result-ReactomeAnalysisResult-method0.230.000.21
get_result0.190.010.21
names-ReactomeAnalysisResult-method0.140.020.15
open_reactome-ReactomeAnalysisResult-method0.200.000.21
open_reactome0.140.020.15
pathways-ReactomeAnalysisResult-method1.190.011.21
pathways1.050.031.09
perform_reactome_analysis 2.15 0.0316.73
plot_correlations-ReactomeAnalysisResult-method1.380.041.41
plot_correlations1.580.031.61
plot_gsva_heatmap-ReactomeAnalysisResult-method31.29 0.9891.59
plot_gsva_heatmap30.81 1.2891.41
plot_gsva_pathway-ReactomeAnalysisResult-method31.78 1.4688.86
plot_gsva_pathway32.89 1.2691.31
plot_gsva_pca-ReactomeAnalysisResult-method30.94 1.0294.02
plot_gsva_pca30.31 1.1587.11
plot_heatmap-ReactomeAnalysisResult-method1.340.021.36
plot_heatmap1.350.011.36
plot_volcano-ReactomeAnalysisResult-method0.170.000.17
plot_volcano0.170.000.17
print-ReactomeAnalysisRequest-method0.020.000.02
print-ReactomeAnalysisResult-method0.150.000.15
reactome_links-ReactomeAnalysisResult-method0.150.000.15
reactome_links0.180.000.18
result_types-ReactomeAnalysisResult-method0.170.000.17
result_types0.170.020.19
set_method-ReactomeAnalysisRequest-method000
set_method0.000.020.01
set_parameters-ReactomeAnalysisRequest-method000
set_parameters000
show-ReactomeAnalysisRequest-method000
show-ReactomeAnalysisResult-method0.200.010.22