Package: genomes

Version: 2.3.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.3.1.tar.gz

StartedAt: 2012-06-21 00:16:28 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:17:33 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 65.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: genomes.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/genomes.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 'genomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomes' version '2.3.1'
* 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 whether package 'genomes' 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 'genomes-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enaSubmission
> ### Title: ENA SRA submission dates
> ### Aliases: enaSubmission
> ### Keywords: methods
> 
> ### ** Examples
> 
> #compare to http://www.ebi.ac.uk/ena/data/view/ERA000746
> enaSubmission("ERA000746")
Opening and ending tag mismatch: ROOT line 2 and SUBMISSION
Extra content at the end of the document
Error: 1: Opening and ending tag mismatch: ROOT line 2 and SUBMISSION
2: Extra content at the end of the document
Execution halted

* installing *source* package 'genomes' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'genome-tables.Rnw' 
** testing if installed package can be loaded

* DONE (genomes)

name	user	system	elapsed
complete	0.076	0.009	0.086
doublingTime	0.370	0.015	0.384
efetch	0.017	0.007	1.511
einfo	0.102	0.006	0.638
elink	0.092	0.005	1.703
enaExperiment	3.223	0.027	8.034
enaFiles	0.019	0.003	0.842
enaProject	0.116	0.002	0.667
enaSRA	2.536	0.015	4.301
enaStudy	3.126	0.022	6.867