Package: doseR

Version: 0.99.15

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings doseR_0.99.15.tar.gz

StartedAt: 2019-04-09 02:24:03 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:28:04 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 241.3 seconds

RetCode: 0

Status:  OK

CheckDir: doseR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doseR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings doseR_0.99.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/doseR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'doseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'doseR' version '0.99.15'
* 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 'doseR' 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running '1.R'
 OK
** running tests for arch 'x64' ...
  Running '1.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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/doseR_0.99.15.tar.gz && rm -rf doseR.buildbin-libdir && mkdir doseR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=doseR.buildbin-libdir doseR_0.99.15.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL doseR_0.99.15.zip && rm doseR_0.99.15.tar.gz doseR_0.99.15.zip
###
##############################################################################
##############################################################################


  % 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  783k  100  783k    0     0  1961k      0 --:--:-- --:--:-- --:--:-- 1994k

install for i386

* installing *source* package 'doseR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'doseR'
    finding HTML links ... done
    dafs                                    html  
    dafsFilter                              html  
    generateStats                           html  
    getLibsizes3                            html  
    glSeq                                   html  
    hmel.dat                                html  
    iqrxFilter                              html  
    make_RPKM                               html  
    plotExpr                                html  
    plotMA.se                               html  
    plotRatioBoxes                          html  
    plotRatioDensity                        html  
    quantFilter                             html  
    se.DM                                   html  
    se                                      html  
    simpleFilter                            html  
    test_diffs                              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 'doseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'doseR' as doseR_0.99.15.zip
* DONE (doseR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'doseR' successfully unpacked and MD5 sums checked

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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(doseR)
> 
> data(hmel.se)
> f_se <- quantFilter(se, lo.bound = 0.4, hi.bound = 0.5)
Filtering removed 12660 (92.96%) of 13619 total loci.
> dm <- se.DM(f_se)
> temp <- glSeq(dm, "-1 + replicate")
> 
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[4], 1), round(6.008, 1))
[1] TRUE
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[5], 1), round(5.840, 1))
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  11.54    0.87   12.40 

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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(doseR)
> 
> data(hmel.se)
> f_se <- quantFilter(se, lo.bound = 0.4, hi.bound = 0.5)
Filtering removed 12660 (92.96%) of 13619 total loci.
> dm <- se.DM(f_se)
> temp <- glSeq(dm, "-1 + replicate")
> 
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[4], 1), round(6.008, 1))
[1] TRUE
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[5], 1), round(5.840, 1))
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  10.48    0.35   10.82