BioC 3.4: CHECK report for arrayQualityMetrics on malbec1

Package: arrayQualityMetrics

Version: 3.30.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings arrayQualityMetrics_3.30.0.tar.gz

StartedAt: 2017-04-14 21:00:33 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:02:56 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 143.0 seconds

RetCode: 0

Status:  OK

CheckDir: arrayQualityMetrics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings arrayQualityMetrics_3.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/arrayQualityMetrics.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘arrayQualityMetrics/DESCRIPTION’ ... OK
* this is package ‘arrayQualityMetrics’ version ‘3.30.0’
* 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 ‘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.boxplot: no visible global function definition for ‘new’
aqm.density: no visible global function definition for ‘new’
aqm.heatmap: no visible global function definition for ‘new’
aqm.maplot: no visible global function definition for ‘new’
aqm.meansd: no visible global function definition for ‘new’
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.outliers: no visible global function definition for ‘new’
aqm.pca: no visible global function definition for ‘prcomp’
aqm.pca: no visible global function definition for ‘na.omit’
aqm.pca: no visible global function definition for ‘new’
aqm.pmmm : PMMM: no visible global function definition for ‘lines’
aqm.pmmm: no visible global function definition for ‘new’
aqm.probesmap: no visible binding for global variable ‘hasTarget’
aqm.probesmap: no visible global function definition for ‘new’
aqm.rnadeg: no visible global function definition for ‘new’
aqm.writereport: no visible binding for global variable ‘slot’
outliers: no visible global function definition for ‘ecdf’
outliers : <anonymous>: no visible global function definition for
  ‘ks.test’
outliers: no visible global function definition for ‘new’
reportModule: no visible global function definition for ‘validObject’
spatialplot: no visible global function definition for ‘new’
Undefined global functions or variables:
  abline ecdf hasTarget ks.test lines na.omit new par prcomp segments
  slot text validObject
Consider adding
  importFrom("graphics", "abline", "lines", "par", "segments", "text")
  importFrom("methods", "new", "slot", "validObject")
  importFrom("stats", "ecdf", "ks.test", "na.omit", "prcomp")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/arrayQualityMetrics.Rcheck/00check.log’
for details.

* installing *source* package ‘arrayQualityMetrics’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (arrayQualityMetrics)