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BioC 3.0: CHECK report for ArrayExpress on oaxaca

This page was generated on 2015-04-10 10:03:15 -0700 (Fri, 10 Apr 2015).

Package 49/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.26.0
Ibrahim Emam
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ArrayExpress
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: ArrayExpress
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayExpress_1.26.0.tar.gz
StartedAt: 2015-04-09 21:25:19 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:28:10 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 170.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpress.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayExpress_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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/5s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/117s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ArrayExpress 10.025  1.166  86.254
getAE         4.340  0.396  21.121
queryAE       3.437  0.081   6.774
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.

ArrayExpress.Rcheck/00install.out:

* 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)

ArrayExpress.Rcheck/ArrayExpress-Ex.timings:

nameusersystemelapsed
ArrayExpress10.025 1.16686.254
ae2bioc0.0010.0000.001
getAE 4.340 0.39621.121
procset0.0000.0000.001
queryAE3.4370.0816.774