Package: genomes

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.2.0.tar.gz

StartedAt: 2012-09-24 00:17:39 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:19:05 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 86.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: genomes.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/genomes.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '2.2.0'
* 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 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: ncbiTaxonomy
> ### Title: NCBI taxonomy database
> ### Aliases: ncbiTaxonomy
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> ncbiTaxonomy(c("Bacillus anthracis", "Yersinia pestis"))
[1] "WARNING: please set your email using Sys.setenv(email='name@email.com')"
[1] "WARNING: please set your email using Sys.setenv(email='name@email.com')"
[1] "2 results found"
Error in names(x) <- c("id", "rank", "division", "name", "common", "taxid",  : 
  'names' attribute [14] must be the same length as the vector [12]
Calls: ncbiTaxonomy
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	0.056	0.007	0.062
doublingTime	0.288	0.012	0.300
efetch	0.015	0.006	1.502
einfo	0.078	0.005	0.585
elink	0.087	0.004	1.945
enaExperiment	4.182	0.027	10.753
enaFiles	0.017	0.002	0.807
enaProject	0.109	0.001	0.537
enaSRA	2.374	0.009	4.677
enaStudy	3.004	0.015	6.984
enaSubmission	0.005	0.000	0.364
enaTaxonomy	0.015	0.002	1.479
esearch	0.025	0.002	0.917
esummary	0.153	0.004	1.232
genomes-lines	0.264	0.016	0.279
genomes-plot	0.284	0.016	0.301
genomes-print	0.150	0.007	0.158
genomes-subset	0.138	0.005	0.143
genomes-summary	0.025	0.001	0.025
genomes-update	0.002	0.003	0.005
genomes	0.320	0.020	0.341
genus	0.296	0.008	0.305
image2	0.385	0.013	0.399
lenvs	0.024	0.003	0.027
leuks	0.076	0.006	0.082
like	0.220	0.011	0.233
lproks	0.481	0.033	0.514
ncbiGenome	0.095	0.004	2.415
ncbiNucleotide	0.579	0.006	2.301
ncbiProject	0.971	0.011	2.357
ncbiPubmed	0.231	0.007	0.739
ncbiRelease	0.016	0.002	1.100
ncbiSubmit	0.131	0.005	2.323