BioC 3.2: CHECK report for CopyNumber450k on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CopyNumber450k_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CopyNumber450k.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CopyNumber450k/DESCRIPTION’ ... OK
* this is package ‘CopyNumber450k’ version ‘1.6.0’
* 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 ‘CopyNumber450k’ can be installed ... [24s/24s] WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘plotPCA’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/CopyNumber450k.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
* 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
extractFromRGChannelSet450k: no visible global function definition for
  ‘seqnames’
* 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 ... [70s/73s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
CNV450kSet 53.476  5.134  62.308
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CopyNumber450k.Rcheck/00check.log’
for details.

* installing *source* package ‘CopyNumber450k’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Creating a new generic function for ‘plotSample’ in package ‘CopyNumber450k’
Creating a new generic function for ‘plotPCA’ in package ‘CopyNumber450k’
Creating a generic function for ‘write.csv’ from package ‘utils’ in package ‘CopyNumber450k’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Warning: multiple methods tables found for ‘plotPCA’
* DONE (CopyNumber450k)

BioC 3.2: CHECK report for CopyNumber450k on oaxaca

Summary

Command output