BioC 3.0: CHECK report for ArrayExpress on zin1

Package: ArrayExpress

Version: 1.26.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpress_1.26.0.tar.gz

StartedAt: 2015-04-09 21:36:23 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:38:21 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 118.5 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayExpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpress_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.26.0’
* 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 ‘ArrayExpress’ can be installed ... [4s/4s] 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
Package in Depends field not imported from: ‘Biobase’
  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
ae2bioc: no visible global function definition for ‘varLabels’
ae2bioc: no visible global function definition for ‘pData’
ae2bioc: no visible global function definition for ‘sampleNames’
ae2bioc: no visible global function definition for ‘phenoData<-’
ae2bioc: no visible global function definition for ‘protocolData’
ae2bioc: no visible global function definition for ‘sampleNames<-’
ae2bioc: no visible global function definition for ‘protocolData<-’
ae2bioc: no visible global function definition for ‘experimentData<-’
ae2bioc: no visible global function definition for ‘featureData<-’
ae2bioc: no visible global function definition for ‘featureNames’
ae2bioc: no visible global function definition for ‘featureData’
getAE: no visible global function definition for
  ‘read.AnnotatedDataFrame’
getAE: no visible global function definition for ‘pData’
getAE: no visible global function definition for ‘varLabels’
getPhenoDataPerAD: no visible global function definition for ‘pData’
getPhenoDataPerAD: no visible global function definition for
  ‘varLabels’
getcolproc: no visible global function definition for
  ‘read.AnnotatedDataFrame’
getcolproc: no visible global function definition for ‘varLabels’
isOneChannel: no visible global function definition for
  ‘read.AnnotatedDataFrame’
isOneChannel: no visible global function definition for ‘varLabels’
preparePhenoDataFor2channel: no visible global function definition for
  ‘pData’
preparePhenoDataFor2channel: no visible global function definition for
  ‘varLabels’
preparePhenoDataFor2channel: no visible global function definition for
  ‘pData<-’
readPhenoData: no visible global function definition for
  ‘read.AnnotatedDataFrame’
readPhenoData: no visible global function definition for ‘pData’
readPhenoData : <anonymous>: no visible global function definition for
  ‘pData’
readPhenoData: no visible global function definition for ‘pData<-’
readPhenoData: no visible global function definition for ‘varLabels’
* 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 ... [16s/78s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ArrayExpress 8.212  0.644  50.681
queryAE      2.988  0.008   6.836
getAE        2.300  0.156  18.682
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ArrayExpress	8.212	0.644	50.681
ae2bioc	0.000	0.000	0.001
getAE	2.300	0.156	18.682
procset	0	0	0
queryAE	2.988	0.008	6.836