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CHECK report for Doscheda on tokay1

This page was generated on 2021-05-06 12:30:59 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the Doscheda package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 504/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Doscheda 1.12.0  (landing page)
Bruno Contrino
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Doscheda
Branch: RELEASE_3_12
Last Commit: cac45a7
Last Changed Date: 2020-10-27 11:26:50 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Doscheda
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Doscheda.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Doscheda_1.12.0.tar.gz
StartedAt: 2021-05-06 02:21:00 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:26:13 -0400 (Thu, 06 May 2021)
EllapsedTime: 312.6 seconds
RetCode: 0
Status:   OK   
CheckDir: Doscheda.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Doscheda.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Doscheda_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Doscheda.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Doscheda/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Doscheda' 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
fitModel-methods 21.95   0.46   24.28
runDoscheda      17.93   0.00   19.17
pcaPlot-methods   5.73   0.13    7.70
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
fitModel-methods 21.26   0.64   23.82
runDoscheda      18.32   0.02   19.39
pcaPlot-methods   5.95   0.06    8.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Doscheda_1.12.0.tar.gz && rm -rf Doscheda.buildbin-libdir && mkdir Doscheda.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Doscheda.buildbin-libdir Doscheda_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Doscheda_1.12.0.zip && rm Doscheda_1.12.0.tar.gz Doscheda_1.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 16 2863k   16  475k    0     0  25.0M      0 --:--:-- --:--:-- --:--:-- 25.8M
100 2863k  100 2863k    0     0  42.8M      0 --:--:-- --:--:-- --:--:-- 43.0M

install for i386

* 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
  converting help for package 'Doscheda'
    finding HTML links ... done
    ChemoProtSet-class                      html  
    boxplot-ChemoProtSet-method             html  
    corrPlot-methods                        html  
    densityPlot-methods                     html  
    doscheda                                html  
    doschedaApp                             html  
    doschedaData                            html  
    fitModel-methods                        html  
    getDatasets-methods                     html  
    getFinal-methods                        html  
    getInput-methods                        html  
    getNorm-methods                         html  
    getParameters-methods                   html  
    makeReport                              html  
    meanSdPlot-methods                      html  
    pcaPlot-methods                         html  
    plot.ChemoProtSet                       html  
    processedExample                        html  
    removePeptides-methods                  html  
    replicatePlot-methods                   html  
    runDoscheda                             html  
    runNormalisation-methods                html  
    setData-methods                         html  
    setParameters-methods                   html  
    volcanoPlot-methods                     html  
** 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

install for x64

* installing *source* package 'Doscheda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Doscheda' as Doscheda_1.12.0.zip
* DONE (Doscheda)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Doscheda' successfully unpacked and MD5 sums checked

Tests output

Doscheda.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   4.70    0.43    6.87 

Doscheda.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(Doscheda)
> 
> test_check("Doscheda")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   6.84    0.54    8.89 

Example timings

Doscheda.Rcheck/examples_i386/Doscheda-Ex.timings

nameusersystemelapsed
corrPlot-methods2.220.163.98
densityPlot-methods1.970.033.02
doschedaData0.060.000.07
fitModel-methods21.95 0.4624.28
getDatasets-methods000
getFinal-methods000
getInput-methods000
getNorm-methods0.000.010.01
getParameters-methods000
makeReport000
meanSdPlot-methods2.240.033.22
pcaPlot-methods5.730.137.70
processedExample0.080.000.08
removePeptides-methods000
replicatePlot-methods2.250.013.17
runDoscheda17.93 0.0019.17
runNormalisation-methods2.550.133.69
setData-methods0.440.120.56
setParameters-methods000
volcanoPlot-methods1.930.073.02

Doscheda.Rcheck/examples_x64/Doscheda-Ex.timings

nameusersystemelapsed
corrPlot-methods2.220.033.86
densityPlot-methods2.470.033.42
doschedaData0.050.000.05
fitModel-methods21.26 0.6423.82
getDatasets-methods000
getFinal-methods000
getInput-methods000
getNorm-methods000
getParameters-methods000
makeReport000
meanSdPlot-methods3.350.054.49
pcaPlot-methods5.950.068.01
processedExample0.080.000.08
removePeptides-methods000
replicatePlot-methods2.330.033.38
runDoscheda18.32 0.0219.39
runNormalisation-methods2.950.204.18
setData-methods0.370.240.61
setParameters-methods000
volcanoPlot-methods2.790.063.85