Package: OncoScore

Version: 1.6.2

Command: rm -rf OncoScore.buildbin-libdir OncoScore.Rcheck && mkdir OncoScore.buildbin-libdir OncoScore.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OncoScore.buildbin-libdir OncoScore_1.6.2.tar.gz >OncoScore.Rcheck\00install.out 2>&1 && cp OncoScore.Rcheck\00install.out OncoScore-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=OncoScore.buildbin-libdir --install="check:OncoScore-install.out" --force-multiarch --no-vignettes --timings OncoScore_1.6.2.tar.gz

StartedAt: 2018-04-12 01:54:26 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:56:19 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 113.6 seconds

RetCode: 0

Status:  OK

CheckDir: OncoScore.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf OncoScore.buildbin-libdir OncoScore.Rcheck && mkdir OncoScore.buildbin-libdir OncoScore.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OncoScore.buildbin-libdir OncoScore_1.6.2.tar.gz >OncoScore.Rcheck\00install.out 2>&1 && cp OncoScore.Rcheck\00install.out OncoScore-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=OncoScore.buildbin-libdir --install="check:OncoScore-install.out" --force-multiarch --no-vignettes --timings OncoScore_1.6.2.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/OncoScore.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OncoScore/DESCRIPTION' ... OK
* this is package 'OncoScore' version '1.6.2'
* 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 'OncoScore' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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

install for i386

* installing *source* package 'OncoScore' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'OncoScore'
    finding HTML links ... done
    combine.query.results                   html  
    combine.single.matrix                   html  
    compute.frequencies.scores              html  
    compute.oncoscore                       html  
    compute.oncoscore.from.region           html  
    compute.oncoscore.timeseries            html  
    estimate.oncogenes                      html  
    genes                                   html  
    get.genes.from.biomart                  html  
    get.list.from.xml                       html  
    get.pubmed.driver.analysis              html  
    perform.query                           html  
    perform.query.from.region               html  
    perform.query.timeseries                html  
    plot.oncoscore                          html  
    plot.oncoscore.timeseries               html  
    query                                   html  
    query.timepoints                        html  
    timepoints                              html  
    try.scan                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'OncoScore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OncoScore' as OncoScore_1.6.2.zip
* DONE (OncoScore)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(OncoScore)
> 
> test_check("OncoScore")
== testthat results  ===========================================================
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.20    0.06    4.07 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(OncoScore)
> 
> test_check("OncoScore")
== testthat results  ===========================================================
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.03    0.06    3.09