Package: RefPlus

Version: 1.48.0

Command: rm -rf RefPlus.buildbin-libdir RefPlus.Rcheck && mkdir RefPlus.buildbin-libdir RefPlus.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefPlus.buildbin-libdir RefPlus_1.48.0.tar.gz >RefPlus.Rcheck\00install.out 2>&1 && cp RefPlus.Rcheck\00install.out RefPlus-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RefPlus.buildbin-libdir --install="check:RefPlus-install.out" --force-multiarch --no-vignettes --timings RefPlus_1.48.0.tar.gz

StartedAt: 2018-04-12 02:34:38 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:37:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 164.7 seconds

RetCode: 0

Status:  OK

CheckDir: RefPlus.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf RefPlus.buildbin-libdir RefPlus.Rcheck && mkdir RefPlus.buildbin-libdir RefPlus.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RefPlus.buildbin-libdir RefPlus_1.48.0.tar.gz >RefPlus.Rcheck\00install.out 2>&1 && cp RefPlus.Rcheck\00install.out RefPlus-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RefPlus.buildbin-libdir --install="check:RefPlus-install.out" --force-multiarch --no-vignettes --timings RefPlus_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RefPlus.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 'RefPlus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RefPlus' version '1.48.0'
* 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 'RefPlus' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: 'affyPLM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rma.para: no visible global function definition for 'rmaPLM'
rma.para: no visible global function definition for 'coefs.probe'
rma.para: no visible global function definition for 'coefs'
Undefined global functions or variables:
  coefs coefs.probe rmaPLM
* checking Rd files ... NOTE
prepare_Rd: colMedians.Rd:19: Dropping empty section \references
prepare_Rd: rmaref.predict.Rd:29-30: Dropping empty section \examples
* 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
RefPlus-package 13.45   0.44   14.02
rmaplus         11.30   0.29   11.59
rma.para         8.08   0.12    8.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
RefPlus-package 12.56   0.33   12.94
rmaplus          8.94   0.19    9.12
rma.para         6.45   0.21    6.67
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/RefPlus.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RefPlus' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'RefPlus'
    finding HTML links ... done
    RefPlus-package                         html  
    colMedians                              html  
    normalize.quantiles2                    html  
    rma.para                                html  
    rmaplus                                 html  
    rmaref.predict                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RefPlus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RefPlus' as RefPlus_1.48.0.zip
* DONE (RefPlus)
In R CMD INSTALL
In R CMD INSTALL