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CHECK report for RIVER on tokay1

This page was generated on 2018-04-12 13:29:41 -0400 (Thu, 12 Apr 2018).

Package 1184/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIVER 1.2.0
Yungil Kim
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RIVER
Branch: RELEASE_3_6
Last Commit: 656eb6e
Last Changed Date: 2017-10-30 12:41:27 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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.



Installation output

RIVER.Rcheck/00install.out


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

Tests output

RIVER.Rcheck/tests_i386/testthat.Rout


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 

RIVER.Rcheck/tests_x64/testthat.Rout


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 

Example timings

RIVER.Rcheck/examples_i386/RIVER-Ex.timings

nameusersystemelapsed
appRIVER4.150.124.31
evaRIVER4.130.044.19
getData0.390.000.39
getFuncRvFeat1.080.001.07
getFuncRvPosteriors101
integratedEM3.260.033.30
mleBeta1.050.001.05
mleTheta1.170.011.19
plotPosteriors4.250.064.31
testPosteriors3.440.053.48

RIVER.Rcheck/examples_x64/RIVER-Ex.timings

nameusersystemelapsed
appRIVER3.970.094.06
evaRIVER4.030.054.19
getData0.340.000.35
getFuncRvFeat1.140.031.17
getFuncRvPosteriors1.050.021.06
integratedEM3.300.083.38
mleBeta1.010.011.03
mleTheta1.000.021.01
plotPosteriors4.330.124.46
testPosteriors3.250.073.31