Package: annotate

Version: 1.35.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotate_1.35.2.tar.gz

StartedAt: 2012-06-20 21:43:34 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 21:46:40 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 185.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: annotate.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/annotate.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.35.2'
* 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 whether package 'annotate' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'annotate-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accessionToUID
> ### Title: A function to convert accession values to NCBI UIDs.
> ### Aliases: accessionToUID
> ### Keywords: interface
> 
> ### ** Examples
> 
> 
>      ## The two returns from genbank should be the same
>      xdoc <- genbank("U03397",type="accession",disp="data")
Warning in file(file, "r") :
  cannot open: HTTP status was '404 Not Found'
Error in file(file, "r") : cannot open the connection
Calls: genbank ... .transformAccession -> accessionToUID -> paste -> scan -> file
Execution halted

* installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GOusage.Rnw' 
   'annotate.Rnw' 
   'chromLoc.Rnw' 
   'prettyOutput.Rnw' 
   'query.Rnw' 
   'useDataPkgs.Rnw' 
   'useHomology.Rnw' 
   'useProbeInfo.Rnw' 
** testing if installed package can be loaded

* DONE (annotate)

name	user	system	elapsed
ACCNUMStats	4.217	0.094	4.410
GO2heatmap	0.344	0.026	0.373
GOmnplot	0.238	0.013	0.251
HTMLPage-class	0	0	0
LL2homology	0.000	0.000	0.001
PMIDAmat	0.301	0.021	0.467
PWAmat	8.659	0.266	8.983
UniGeneQuery	0.003	0.000	0.002