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CHECK report for DEFormats on tokay1

This page was generated on 2021-05-06 12:30:39 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the DEFormats package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 444/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEFormats 1.18.0  (landing page)
Andrzej OleĊ›
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/DEFormats
Branch: RELEASE_3_12
Last Commit: 5297c56
Last Changed Date: 2020-10-27 11:13:03 -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: DEFormats
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEFormats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEFormats_1.18.0.tar.gz
StartedAt: 2021-05-06 02:03:21 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:08:08 -0400 (Thu, 06 May 2021)
EllapsedTime: 287.5 seconds
RetCode: 0
Status:   OK   
CheckDir: DEFormats.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:DEFormats.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DEFormats_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DEFormats.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 'DEFormats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DEFormats' version '1.18.0'
* 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 'DEFormats' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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

DEFormats.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/DEFormats_1.18.0.tar.gz && rm -rf DEFormats.buildbin-libdir && mkdir DEFormats.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEFormats.buildbin-libdir DEFormats_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DEFormats_1.18.0.zip && rm DEFormats_1.18.0.tar.gz DEFormats_1.18.0.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
100  9106  100  9106    0     0   422k      0 --:--:-- --:--:-- --:--:--  444k

install for i386

* installing *source* package 'DEFormats' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'DGEList' from 'edgeR' in package 'DEFormats'
    (from the saved implicit definition)
** help
*** installing help indices
  converting help for package 'DEFormats'
    finding HTML links ... done
    DEFormats                               html  
    finding level-2 HTML links ... done

    DGEList                                 html  
    as.DESeqDataSet                         html  
    as.DGEList                              html  
    simulateNormFactors                     html  
    simulateRnaSeqData                      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 'DEFormats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEFormats' as DEFormats_1.18.0.zip
* DONE (DEFormats)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DEFormats' successfully unpacked and MD5 sums checked

Tests output

DEFormats.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(DEFormats)
> 
> test_check("DEFormats")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
  14.70    1.00   15.67 

DEFormats.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(DEFormats)
> 
> test_check("DEFormats")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
  17.21    0.62   17.82 

Example timings

DEFormats.Rcheck/examples_i386/DEFormats-Ex.timings

nameusersystemelapsed
DGEList0.390.000.39
as.DESeqDataSet0.440.010.46
as.DGEList0.440.030.47
simulateNormFactors0.430.020.45
simulateRnaSeqData0.260.000.26

DEFormats.Rcheck/examples_x64/DEFormats-Ex.timings

nameusersystemelapsed
DGEList0.740.000.73
as.DESeqDataSet1.480.001.49
as.DGEList0.790.030.83
simulateNormFactors0.750.140.89
simulateRnaSeqData0.550.010.56