BioC 3.2: CHECK report for ArrayExpress on zin1

Package: ArrayExpress

Version: 1.29.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpress_1.29.1.tar.gz

StartedAt: 2015-08-23 21:42:14 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 21:43:58 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 103.8 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayExpress.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpress_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.29.1’
* 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 ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/75s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
ArrayExpress 6.434  0.466  49.002
queryAE      2.231  0.045   6.148
getAE        1.828  0.131  18.113
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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	6.434	0.466	49.002
ae2bioc	0.001	0.000	0.000
getAE	1.828	0.131	18.113
procset	0	0	0
queryAE	2.231	0.045	6.148