Package: RIVER

Version: 1.2.0

Command: rm -rf RIVER.buildbin-libdir RIVER.Rcheck && mkdir RIVER.buildbin-libdir RIVER.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIVER.buildbin-libdir RIVER_1.2.0.tar.gz >RIVER.Rcheck\00install.out 2>&1 && cp RIVER.Rcheck\00install.out RIVER-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RIVER.buildbin-libdir --install="check:RIVER-install.out" --force-multiarch --no-vignettes --timings RIVER_1.2.0.tar.gz

StartedAt: 2018-04-12 02:42:57 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:45:42 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 164.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RIVER.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf RIVER.buildbin-libdir RIVER.Rcheck && mkdir RIVER.buildbin-libdir RIVER.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIVER.buildbin-libdir RIVER_1.2.0.tar.gz >RIVER.Rcheck\00install.out 2>&1 && cp RIVER.Rcheck\00install.out RIVER-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RIVER.buildbin-libdir --install="check:RIVER-install.out" --force-multiarch --no-vignettes --timings RIVER_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RIVER.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 'RIVER/DESCRIPTION' ... OK
* this is package 'RIVER' version '1.2.0'
* 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 'RIVER' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Jv7Qz/R.INSTALL3af01a5fc68/RIVER/man/getData.Rd:38: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RIVER.Rcheck/00install.out' for details.
* 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 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/RIVER.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RIVER' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'RIVER'
    finding HTML links ... done
    RIVER                                   html  
    appRIVER                                html  
    evaRIVER                                html  
    getData                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6Jv7Qz/R.INSTALL3af01a5fc68/RIVER/man/getData.Rd:38: missing file link 'ExpressionSet'
    getFuncRvFeat                           html  
    getFuncRvPosteriors                     html  
    integratedEM                            html  
    mleBeta                                 html  
    mleTheta                                html  
    plotPosteriors                          html  
    testPosteriors                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RIVER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIVER' as RIVER_1.2.0.zip
* DONE (RIVER)
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.

> library(testthat)
> library(RIVER)
> 
> test_check("RIVER")
 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


== testthat results  ===========================================================
OK: 33 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.40    0.48   17.87 

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.

> library(testthat)
> library(RIVER)
> 
> test_check("RIVER")
 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


 ::: EM iteration is terminated since it converges within a
        predefined tolerance (0.001) ::: 


== testthat results  ===========================================================
OK: 33 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  18.51    0.35   18.85