Multiple platform build/check report for BioC 3.10 - CHECK report for Doscheda on tokay1

Package: Doscheda

Version: 1.8.1

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Doscheda.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Doscheda_1.8.1.tar.gz

StartedAt: 2020-04-15 02:47:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:52:10 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 289.3 seconds

RetCode: 0

Status: OK

CheckDir: Doscheda.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Doscheda.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Doscheda_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Doscheda.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.8.1'
* 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 or elapsed time > 5s
                  user system elapsed
fitModel-methods 20.20   0.43   22.76
runDoscheda      18.11   0.19   19.29
pcaPlot-methods   4.61   0.05    6.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
fitModel-methods 24.38   0.67   27.02
runDoscheda      16.75   0.03   17.94
pcaPlot-methods   6.23   0.07    8.48
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Doscheda_1.8.1.tar.gz && rm -rf Doscheda.buildbin-libdir && mkdir Doscheda.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Doscheda.buildbin-libdir Doscheda_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Doscheda_1.8.1.zip && rm Doscheda_1.8.1.tar.gz Doscheda_1.8.1.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
 31 2863k   31  896k    0     0  2281k      0  0:00:01 --:--:--  0:00:01 2303k
100 2863k  100 2863k    0     0  5128k      0 --:--:-- --:--:-- --:--:-- 5159k

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_1.8.1.zip
* DONE (Doscheda)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Doscheda' successfully unpacked and MD5 sums checked


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.62    0.50    6.57


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   6.79    0.35   15.04

name	user	system	elapsed
corrPlot-methods	2.11	0.13	3.79
densityPlot-methods	1.81	0.05	2.90
doschedaData	0.03	0.00	0.03
fitModel-methods	20.20	0.43	22.76
getDatasets-methods	0	0	0
getFinal-methods	0	0	0
getInput-methods	0	0	0
getNorm-methods	0	0	0
getParameters-methods	0	0	0
makeReport	0	0	0
meanSdPlot-methods	2.19	0.05	3.19
pcaPlot-methods	4.61	0.05	6.56
processedExample	0.06	0.00	0.07
removePeptides-methods	0	0	0
replicatePlot-methods	1.88	0.01	2.83
runDoscheda	18.11	0.19	19.29
runNormalisation-methods	2.22	0.30	3.47
setData-methods	0.42	0.12	0.55
setParameters-methods	0	0	0
volcanoPlot-methods	2.09	0.03	3.19

name	user	system	elapsed
corrPlot-methods	2.28	0.05	3.84
densityPlot-methods	2.44	0.02	3.49
doschedaData	0.05	0.00	0.05
fitModel-methods	24.38	0.67	27.02
getDatasets-methods	0	0	0
getFinal-methods	0	0	0
getInput-methods	0	0	0
getNorm-methods	0.01	0.00	0.01
getParameters-methods	0	0	0
makeReport	0	0	0
meanSdPlot-methods	2.49	0.01	3.58
pcaPlot-methods	6.23	0.07	8.48
processedExample	0.06	0.00	0.07
removePeptides-methods	0	0	0
replicatePlot-methods	2.17	0.00	3.28
runDoscheda	16.75	0.03	17.94
runNormalisation-methods	2.56	0.29	3.95
setData-methods	0.55	0.18	0.72
setParameters-methods	0	0	0
volcanoPlot-methods	2.95	0.04	4.19

CHECK report for Doscheda on tokay1

Summary

Command output

Installation output

Tests output

Example timings