Package: BEclear

Version: 1.10.0

Command: rm -rf BEclear.buildbin-libdir BEclear.Rcheck && mkdir BEclear.buildbin-libdir BEclear.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BEclear.buildbin-libdir BEclear_1.10.0.tar.gz >BEclear.Rcheck\00install.out 2>&1 && cp BEclear.Rcheck\00install.out BEclear-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BEclear.buildbin-libdir --install="check:BEclear-install.out" --force-multiarch --no-vignettes --timings BEclear_1.10.0.tar.gz

StartedAt: 2018-04-11 22:25:35 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:28:03 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 147.5 seconds

RetCode: 0

Status:  OK

CheckDir: BEclear.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BEclear.buildbin-libdir BEclear.Rcheck && mkdir BEclear.buildbin-libdir BEclear.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BEclear.buildbin-libdir BEclear_1.10.0.tar.gz >BEclear.Rcheck\00install.out 2>&1 && cp BEclear.Rcheck\00install.out BEclear-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BEclear.buildbin-libdir --install="check:BEclear-install.out" --force-multiarch --no-vignettes --timings BEclear_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BEclear.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 'BEclear/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEclear' version '1.10.0'
* 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 'BEclear' 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 ... NOTE
BEclear : BEclear: no visible global function definition for 'as'
BEclear : BEclear: no visible global function definition for 'rnorm'
BEclear: no visible global function definition for 'write.table'
calcMedians : calcMedians: no visible global function definition for
  'median'
calcPvalues : calcPvals: no visible global function definition for
  'ks.test'
calcPvalues: no visible global function definition for 'p.adjust'
makeBoxplot: no visible global function definition for 'par'
makeBoxplot: no visible global function definition for 'boxplot'
makeBoxplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  as boxplot ks.test median mtext p.adjust par rnorm write.table
Consider adding
  importFrom("graphics", "boxplot", "mtext", "par")
  importFrom("methods", "as")
  importFrom("stats", "ks.test", "median", "p.adjust", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU or elapsed time > 5s
                   user system elapsed
BEclear            0.59   0.05   13.41
correctBatchEffect 0.55   0.03    7.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BEclear              0.83   0.01   18.02
correctBatchEffect   0.71   0.04    8.83
countValuesToPredict 0.14   0.02    5.22
makeBoxplot          0.10   0.05    5.40
clearBEgenes         0.12   0.00    5.33
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BEclear.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BEclear' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BEclear'
    finding HTML links ... done
    BEclear-package                         html  
    BEclear                                 html  
    finding level-2 HTML links ... done

    BEclearData                             html  
    calcMedians                             html  
    calcPvalues                             html  
    calcScore                               html  
    calcSummary                             html  
    clearBEgenes                            html  
    correctBatchEffect                      html  
    countValuesToPredict                    html  
    ex.corrected.data                       html  
    findWrongValues                         html  
    makeBoxplot                             html  
    replaceWrongValues                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BEclear' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEclear' as BEclear_1.10.0.zip
* DONE (BEclear)
In R CMD INSTALL
In R CMD INSTALL