Package: BioCor

Version: 1.2.1

Command: rm -rf BioCor.buildbin-libdir BioCor.Rcheck && mkdir BioCor.buildbin-libdir BioCor.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioCor.buildbin-libdir BioCor_1.2.1.tar.gz >BioCor.Rcheck\00install.out 2>&1 && cp BioCor.Rcheck\00install.out BioCor-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BioCor.buildbin-libdir --install="check:BioCor-install.out" --force-multiarch --no-vignettes --timings BioCor_1.2.1.tar.gz

StartedAt: 2018-04-11 22:29:54 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:31:38 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 104.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BioCor.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BioCor.buildbin-libdir BioCor.Rcheck && mkdir BioCor.buildbin-libdir BioCor.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioCor.buildbin-libdir BioCor_1.2.1.tar.gz >BioCor.Rcheck\00install.out 2>&1 && cp BioCor.Rcheck\00install.out BioCor-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BioCor.buildbin-libdir --install="check:BioCor-install.out" --force-multiarch --no-vignettes --timings BioCor_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioCor.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 'BioCor/DESCRIPTION' ... OK
* this is package 'BioCor' version '1.2.1'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'BioCor' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa2RrbE/R.INSTALL11886eb62bdc/BioCor/man/combineScores.Rd:78: missing file link 'bpparam'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioCor.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
Examples with CPU or elapsed time > 5s
        user system elapsed
geneSim 8.42   0.10    8.52
pathSim 5.72   0.07    5.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
geneSim 8.99   0.31    9.29
pathSim 5.47   0.15    5.63
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BioCor.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BioCor' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BioCor'
    finding HTML links ... done
    AintoB                                  html  
    BioCor-package                          html  
    addSimilarities                         html  
    clusterGeneSim                          html  
    clusterSim                              html  
    combinadic                              html  
    combineScores                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa2RrbE/R.INSTALL11886eb62bdc/BioCor/man/combineScores.Rd:78: missing file link 'bpparam'
    combineSources                          html  
    conversions                             html  
    diceSim                                 html  
    duplicateIndices                        html  
    geneSim                                 html  
    pathSim                                 html  
    removeDup                               html  
    seq2mat                                 html  
    similarities                            html  
    weighted                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BioCor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioCor' as BioCor_1.2.1.zip
* DONE (BioCor)
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(BioCor)
If you use BioCor in published research, please cite:
> 
> test_check("BioCor")
== testthat results  ===========================================================
OK: 252 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.54    0.06    2.59 

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(BioCor)
If you use BioCor in published research, please cite:
> 
> test_check("BioCor")
== testthat results  ===========================================================
OK: 252 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.56    0.10    2.65