Package: ArrayExpress

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayExpress_1.12.1.tar.gz

StartedAt: 2011-10-12 13:24:25 -0700 (Wed, 12 Oct 2011)

EndedAt: 2011-10-12 13:27:50 -0700 (Wed, 12 Oct 2011)

EllapsedTime: 204.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: ArrayExpress.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ArrayExpress.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.12.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ArrayExpress' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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 ... OK
* 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 examples ... ERROR
Running examples in 'ArrayExpress-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ArrayExpress
> ### Title: R objects from ArrayExpress database
> ### Aliases: ArrayExpress
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ETABM25.affybatch = ArrayExpress(input = "E-TABM-25")
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/index.html'
Content type 'text/html;charset=UTF-8' length unknown
opened URL
........
downloaded 8399 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/E-TABM-25.raw.1.zip'
Content type 'application/zip' length 48026722 bytes (45.8 Mb)
opened URL
==========================
downloaded 23.8 Mb

Warning in download.file(paste(exp, ".raw.", i, ".zip", sep = ""), rawdata[[i]],  :
  downloaded length 24986421 != reported length 48026722
Warning in unzip(zipfile = file.path(path[i], topic[i]), exdir = extractpath) :
  error 1 in extracting from zip file
Error in unzip(zipfile = file.path(path[i], topic[i]), list = TRUE, exdir = extractpath) : 
  zip file '/Users/biocbuild/bbs-2.8-bioc/meat/ArrayExpress.Rcheck/E-TABM-25.raw.1.zip' cannot be opened
Calls: ArrayExpress -> getAE -> extract.zip -> lapply -> FUN -> unzip
Execution halted

* installing *source* package 'ArrayExpress' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (ArrayExpress)

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