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This page was generated on 2023-03-21 11:06:48 -0400 (Tue, 21 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4305
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4287
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4286
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 Doscheda on merida1


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? 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 572/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Doscheda 1.21.0  (landing page)
Bruno Contrino
Snapshot Date: 2023-03-20 14:00:22 -0400 (Mon, 20 Mar 2023)
git_url: https://git.bioconductor.org/packages/Doscheda
git_branch: master
git_last_commit: d0929e1
git_last_commit_date: 2022-11-01 11:16:11 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Doscheda
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Doscheda_1.21.0.tar.gz
StartedAt: 2023-03-21 00:57:05 -0400 (Tue, 21 Mar 2023)
EndedAt: 2023-03-21 01:04:35 -0400 (Tue, 21 Mar 2023)
EllapsedTime: 449.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Doscheda.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Doscheda_1.21.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Doscheda.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Doscheda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Doscheda’ version ‘1.21.0’
* 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         48.851  1.716  75.767
runDoscheda              42.678  0.161  64.303
corrPlot-methods          7.985  0.558  14.738
pcaPlot-methods           8.035  0.074  14.246
runNormalisation-methods  4.073  0.623   7.853
meanSdPlot-methods        3.811  0.057   6.923
volcanoPlot-methods       3.333  0.033   5.817
replicatePlot-methods     3.308  0.046   6.122
densityPlot-methods       3.281  0.045   5.656
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Doscheda
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 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(Doscheda)
> 
> test_check("Doscheda")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  9.108   0.562  14.952 

Example timings

Doscheda.Rcheck/Doscheda-Ex.timings

nameusersystemelapsed
corrPlot-methods 7.985 0.55814.738
densityPlot-methods3.2810.0455.656
doschedaData0.0620.0050.087
fitModel-methods48.851 1.71675.767
getDatasets-methods000
getFinal-methods0.0000.0000.001
getInput-methods000
getNorm-methods0.0000.0000.001
getParameters-methods0.0000.0010.001
makeReport0.0010.0000.000
meanSdPlot-methods3.8110.0576.923
pcaPlot-methods 8.035 0.07414.246
processedExample0.1170.0050.181
removePeptides-methods0.0000.0000.001
replicatePlot-methods3.3080.0466.122
runDoscheda42.678 0.16164.303
runNormalisation-methods4.0730.6237.853
setData-methods0.7210.5011.800
setParameters-methods0.0020.0000.011
volcanoPlot-methods3.3330.0335.817