Package: affyContam

Version: 1.36.0

Command: rm -rf affyContam.buildbin-libdir affyContam.Rcheck && mkdir affyContam.buildbin-libdir affyContam.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyContam.buildbin-libdir affyContam_1.36.0.tar.gz >affyContam.Rcheck\00install.out 2>&1 && cp affyContam.Rcheck\00install.out affyContam-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affyContam.buildbin-libdir --install="check:affyContam-install.out" --force-multiarch --no-vignettes --timings affyContam_1.36.0.tar.gz

StartedAt: 2018-04-11 22:04:49 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:08:03 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 193.9 seconds

RetCode: 0

Status:  OK

CheckDir: affyContam.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyContam.buildbin-libdir affyContam.Rcheck && mkdir affyContam.buildbin-libdir affyContam.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyContam.buildbin-libdir affyContam_1.36.0.tar.gz >affyContam.Rcheck\00install.out 2>&1 && cp affyContam.Rcheck\00install.out affyContam-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affyContam.buildbin-libdir --install="check:affyContam-install.out" --force-multiarch --no-vignettes --timings affyContam_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affyContam.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 'affyContam/DESCRIPTION' ... OK
* this is package 'affyContam' version '1.36.0'
* 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 'affyContam' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'affy' 'affydata'
  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
getCircRegion: no visible global function definition for 'annotation'
getCircRegion : <anonymous>: no visible global function definition for
  'xy2indices'
getCircRegion: no visible global function definition for 'exprs'
getRectRegion: no visible global function definition for 'annotation'
getRectRegion : <anonymous>: no visible global function definition for
  'xy2indices'
getRectRegion: no visible global function definition for 'exprs'
setCircRegion: no visible global function definition for 'annotation'
setCircRegion : <anonymous>: no visible global function definition for
  'xy2indices'
setCircRegion: no visible global function definition for 'exprs'
setCircRegion: no visible global function definition for 'exprs<-'
setRectRegion: no visible global function definition for 'annotation'
setRectRegion : <anonymous>: no visible global function definition for
  'xy2indices'
setRectRegion: no visible global function definition for 'exprs'
setRectRegion: no visible global function definition for 'exprs<-'
Undefined global functions or variables:
  annotation exprs exprs<- xy2indices
* 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
setRectRegion 16.8   0.61    17.7
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
setRectRegion 17.92   0.53   18.45
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/affyContam.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'affyContam' ...
** R
** inst
** preparing package for lazy loading
     Package    LibPath                                     Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.6-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** help
*** installing help indices
  converting help for package 'affyContam'
    finding HTML links ... done
    setRectRegion                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
     Package    LibPath                                     Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.6-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
In R CMD INSTALL

install for x64

* installing *source* package 'affyContam' ...
** testing if installed package can be loaded
     Package    LibPath                                     Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.6-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
* MD5 sums
packaged installation of 'affyContam' as affyContam_1.36.0.zip
* DONE (affyContam)
In R CMD INSTALL
In R CMD INSTALL