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This page was generated on 2021-10-15 15:05:39 -0400 (Fri, 15 Oct 2021).

CHECK results for Doscheda on nebbiolo1

To the developers/maintainers of the Doscheda package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Doscheda.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 527/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Doscheda 1.14.0  (landing page)
Bruno Contrino
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Doscheda
git_branch: RELEASE_3_13
git_last_commit: 8a69504
git_last_commit_date: 2021-05-19 12:29:43 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: Doscheda
Version: 1.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Doscheda_1.14.0.tar.gz
StartedAt: 2021-10-14 09:38:45 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:41:23 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 158.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Doscheda.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Doscheda_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Doscheda.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Doscheda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Doscheda’ version ‘1.14.0’
* 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 ‘Doscheda’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
fitModel-methods 15.278  2.364  21.001
runDoscheda      12.487  0.035  14.207
pcaPlot-methods   4.418  0.125   7.889
corrPlot-methods  2.071  0.049   6.343
* 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: OK


Installation output

Doscheda.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Doscheda
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘Doscheda’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘getInput’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getNorm’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getFinal’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getParameters’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getDatasets’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘boxplot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘corrPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘densityPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
Creating a new generic function for ‘meanSdPlot’ in package ‘Doscheda’
** 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 (Doscheda)

Tests output

Doscheda.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(Doscheda)
> 
> test_check("Doscheda")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  4.625   0.508   8.456 

Example timings

Doscheda.Rcheck/Doscheda-Ex.timings

nameusersystemelapsed
corrPlot-methods2.0710.0496.343
densityPlot-methods1.8160.0043.495
doschedaData0.0260.0080.034
fitModel-methods15.278 2.36421.001
getDatasets-methods0.0000.0000.001
getFinal-methods0.0000.0000.001
getInput-methods000
getNorm-methods0.0000.0000.001
getParameters-methods0.0000.0000.001
makeReport0.0000.0000.001
meanSdPlot-methods2.2480.0283.927
pcaPlot-methods4.4180.1257.889
processedExample0.0520.0120.064
removePeptides-methods0.0010.0000.000
replicatePlot-methods1.7050.0363.375
runDoscheda12.487 0.03514.207
runNormalisation-methods2.0740.9014.618
setData-methods0.3110.7721.083
setParameters-methods0.0000.0020.002
volcanoPlot-methods1.9460.0573.668