BioC 3.3: CHECK report for arrayQualityMetrics on oaxaca

Package: arrayQualityMetrics

Version: 3.28.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings arrayQualityMetrics_3.28.2.tar.gz

StartedAt: 2016-10-12 23:20:31 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:23:19 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 168.0 seconds

RetCode: 0

Status:  OK

CheckDir: arrayQualityMetrics.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 arrayQualityMetrics_3.28.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/arrayQualityMetrics.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘arrayQualityMetrics/DESCRIPTION’ ... OK
* this is package ‘arrayQualityMetrics’ version ‘3.28.2’
* 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 ‘arrayQualityMetrics’ 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aqm.outliers : bp: no visible global function definition for ‘par’
aqm.outliers : bp: no visible global function definition for ‘segments’
aqm.outliers : bp: no visible global function definition for ‘abline’
aqm.outliers : bp: no visible global function definition for ‘text’
aqm.pca: no visible global function definition for ‘prcomp’
aqm.pca: no visible global function definition for ‘na.omit’
aqm.pmmm : PMMM: no visible global function definition for ‘lines’
aqm.probesmap: no visible binding for global variable ‘hasTarget’
outliers: no visible global function definition for ‘ecdf’
outliers : <anonymous>: no visible global function definition for
  ‘ks.test’
Undefined global functions or variables:
  abline ecdf hasTarget ks.test lines na.omit par prcomp segments text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "segments", "text")
  importFrom("stats", "ecdf", "ks.test", "na.omit", "prcomp")
to your NAMESPACE file.
* 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 ... NONE
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/arrayQualityMetrics.Rcheck/00check.log’
for details.

* installing *source* package ‘arrayQualityMetrics’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘boxplot’ from package ‘graphics’ in package ‘affyPLM’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
* DONE (arrayQualityMetrics)