BioC 3.5: CHECK report for affyContam on veracruz2

Package: affyContam

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affyContam_1.34.0.tar.gz

StartedAt: 2017-10-18 00:13:03 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:13:56 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 52.5 seconds

RetCode: 0

Status:  OK

CheckDir: affyContam.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affyContam_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/affyContam.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyContam/DESCRIPTION’ ... OK
* this is package ‘affyContam’ version ‘1.34.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setRectRegion 17.201  0.543  18.303
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/affyContam.Rcheck/00check.log’
for details.

* installing *source* package ‘affyContam’ ...
** R
** inst
** preparing package for lazy loading
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
* DONE (affyContam)

name	user	system	elapsed
setRectRegion	17.201	0.543	18.303