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CHECK report for pwrEWAS on tokay2

This page was generated on 2020-10-17 11:57:31 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE pwrEWAS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1385/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pwrEWAS 1.2.0
Stefan Graw
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pwrEWAS
Branch: RELEASE_3_11
Last Commit: 489ce60
Last Changed Date: 2020-04-27 15:30:32 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pwrEWAS
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pwrEWAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pwrEWAS_1.2.0.tar.gz
StartedAt: 2020-10-17 07:12:16 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:20:23 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 487.5 seconds
RetCode: 0
Status:  OK  
CheckDir: pwrEWAS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pwrEWAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pwrEWAS_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pwrEWAS.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pwrEWAS/DESCRIPTION' ... OK
* this is package 'pwrEWAS' version '1.2.0'
* 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 'pwrEWAS' 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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
pwrEWAS              12.89   1.72   46.06
pwrEWAS_powerPlot    10.39   0.50   39.22
pwrEWAS_deltaDensity  9.71   0.61   38.87
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
pwrEWAS              13.45   1.57   45.52
pwrEWAS_deltaDensity 11.31   0.47   42.23
pwrEWAS_powerPlot    10.66   0.57   40.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

pwrEWAS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pwrEWAS_1.2.0.tar.gz && rm -rf pwrEWAS.buildbin-libdir && mkdir pwrEWAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pwrEWAS.buildbin-libdir pwrEWAS_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pwrEWAS_1.2.0.zip && rm pwrEWAS_1.2.0.tar.gz pwrEWAS_1.2.0.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 52199  100 52199    0     0   860k      0 --:--:-- --:--:-- --:--:--  961k

install for i386

* installing *source* package 'pwrEWAS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pwrEWAS'
    finding HTML links ... done
    pwrEWAS                                 html  
    pwrEWAS_deltaDensity                    html  
    pwrEWAS_powerPlot                       html  
    pwrEWAS_shiny                           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 'pwrEWAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pwrEWAS' as pwrEWAS_1.2.0.zip
* DONE (pwrEWAS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pwrEWAS' successfully unpacked and MD5 sums checked

Tests output

pwrEWAS.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.

> BiocGenerics:::testPackage("pwrEWAS")
snapshotDate(): 2020-04-27
see ?pwrEWAS.data and browseVignettes('pwrEWAS.data') for documentation
loading from cache
[2020-10-17 07:19:18] Finding tau...done [2020-10-17 07:19:25]
[1] "The following taus were chosen: 0.2265625"
[2020-10-17 07:19:25] Running simulation

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[2020-10-17 07:19:25] Running simulation ... done [2020-10-17 07:19:39]


RUNIT TEST PROTOCOL -- Sat Oct 17 07:19:39 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pwrEWAS RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  19.07    1.90   36.04 

pwrEWAS.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.

> BiocGenerics:::testPackage("pwrEWAS")
snapshotDate(): 2020-04-27
see ?pwrEWAS.data and browseVignettes('pwrEWAS.data') for documentation
loading from cache
[2020-10-17 07:19:54] Finding tau...done [2020-10-17 07:20:01]
[1] "The following taus were chosen: 0.224609375"
[2020-10-17 07:20:01] Running simulation

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[2020-10-17 07:20:01] Running simulation ... done [2020-10-17 07:20:15]


RUNIT TEST PROTOCOL -- Sat Oct 17 07:20:15 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pwrEWAS RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  18.76    1.54   34.90 

Example timings

pwrEWAS.Rcheck/examples_i386/pwrEWAS-Ex.timings

nameusersystemelapsed
pwrEWAS12.89 1.7246.06
pwrEWAS_deltaDensity 9.71 0.6138.87
pwrEWAS_powerPlot10.39 0.5039.22
pwrEWAS_shiny000

pwrEWAS.Rcheck/examples_x64/pwrEWAS-Ex.timings

nameusersystemelapsed
pwrEWAS13.45 1.5745.52
pwrEWAS_deltaDensity11.31 0.4742.23
pwrEWAS_powerPlot10.66 0.5740.49
pwrEWAS_shiny000