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CHECK report for RIVER on tokay1

This page was generated on 2019-04-13 11:27:44 -0400 (Sat, 13 Apr 2019).

Package 1317/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIVER 1.6.0
Yungil Kim
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RIVER
Branch: RELEASE_3_8
Last Commit: 9284298
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RIVER
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIVER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RIVER_1.6.0.tar.gz
StartedAt: 2019-04-13 05:04:26 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:07:52 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 206.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RIVER.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIVER.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RIVER_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RIVER.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/Rtmp0EFnEs/R.INSTALL1aec23497399/RIVER/man/getData.Rd:38: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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
* 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
** 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-3.8-bioc/meat/RIVER.Rcheck/00check.log'
for details.



Installation output

RIVER.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RIVER_1.6.0.tar.gz && rm -rf RIVER.buildbin-libdir && mkdir RIVER.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIVER.buildbin-libdir RIVER_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RIVER_1.6.0.zip && rm RIVER_1.6.0.tar.gz RIVER_1.6.0.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 1005k  100 1005k    0     0  19.7M      0 --:--:-- --:--:-- --:--:-- 21.3M

install for i386

* installing *source* package 'RIVER' ...
** R
** inst
** byte-compile and prepare 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-3.8-bioc/tmpdir/Rtmp0EFnEs/R.INSTALL1aec23497399/RIVER/man/getData.Rd:38: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    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_1.6.0.zip
* DONE (RIVER)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RIVER' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RIVER.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(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 
  15.20    0.48   15.68 

RIVER.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(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 
  24.82    0.68   25.50 

Example timings

RIVER.Rcheck/examples_i386/RIVER-Ex.timings

nameusersystemelapsed
appRIVER3.120.113.31
evaRIVER2.780.032.81
getData0.190.000.18
getFuncRvFeat0.870.000.88
getFuncRvPosteriors0.630.020.64
integratedEM3.810.043.86
mleBeta0.810.000.81
mleTheta0.660.020.67
plotPosteriors3.030.013.05
testPosteriors2.650.082.74

RIVER.Rcheck/examples_x64/RIVER-Ex.timings

nameusersystemelapsed
appRIVER2.820.082.89
evaRIVER2.880.032.91
getData0.230.000.23
getFuncRvFeat0.640.020.66
getFuncRvPosteriors0.640.000.64
integratedEM2.610.032.64
mleBeta0.660.000.66
mleTheta0.640.000.64
plotPosteriors3.150.083.23
testPosteriors2.540.092.63