BioC 3.4: CHECK report for convert on morelia

Package: convert

Version: 1.50.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings convert_1.50.0.tar.gz

StartedAt: 2017-04-15 00:24:16 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:24:48 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 32.1 seconds

RetCode: 0

Status:  OK

CheckDir: convert.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 convert_1.50.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/convert.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘convert/DESCRIPTION’ ... OK
* this is package ‘convert’ version ‘1.50.0’
* 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 ‘convert’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘limma’ ‘marray’ ‘methods’
  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
coerce,MAList-ExpressionSet: no visible global function definition for
  ‘new’
coerce,MAList-ExpressionSet: no visible global function definition for
  ‘notes<-’
coerce,MAList-marrayNorm: no visible global function definition for
  ‘new’
coerce,RGList-NChannelSet: no visible global function definition for
  ‘new’
coerce,RGList-NChannelSet: no visible binding for global variable ‘df’
coerce,RGList-marrayRaw: no visible global function definition for
  ‘new’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘new’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘notes<-’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maM’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maLabels’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maGnames’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maInfo’
coerce,marrayNorm-ExpressionSet: no visible global function definition
  for ‘maTargets’
coerce,marrayNorm-MAList: no visible global function definition for
  ‘new’
coerce,marrayNorm-MAList: no visible global function definition for
  ‘getClass’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maRf’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maGf’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maRb’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maGb’
coerce,marrayRaw-NChannelSet: no visible binding for global variable
  ‘assayDataNew’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maInfo’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maTargets’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘new’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maGnames’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘phenoData<-’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘sampleNames’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘sampleNames<-’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘maLabels’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘featureData<-’
coerce,marrayRaw-NChannelSet: no visible global function definition for
  ‘featureNames<-’
coerce,marrayRaw-RGList: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  assayDataNew df featureData<- featureNames<- getClass maGb maGf
  maGnames maInfo maLabels maM maRb maRf maTargets new notes<-
  phenoData<- sampleNames sampleNames<-
Consider adding
  importFrom("methods", "getClass", "new")
  importFrom("stats", "df")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/convert.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
coerce	0.237	0.005	0.243