Package: genomes

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genomes_2.0.0.tar.gz

StartedAt: 2012-03-24 01:21:54 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:24:08 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 134.2 seconds

RetCode: 1

Status:  ERROR

CheckDir: genomes.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/genomes.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '2.0.0'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  complete.rda     56Kb     41Kb       xz
  leuks.rda        49Kb     40Kb       xz
  lproks.rda      307Kb    233Kb       xz
  pub.rda          66Kb     56Kb       xz
  sra.rda         501Kb    324Kb       xz
  virus.rda        83Kb     63Kb       xz
* checking sizes of PDF files under '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: ncbiRelease
> ### Title: NCBI revision history
> ### Aliases: ncbiRelease
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> #Yersinia pestis - 1 chromosome and 3 plasmids
> ncbiRelease("AL590842,AL117189,AL109969,AL117211")
[1] "AL590842 has a common revision history"
[1] "  Finding earliest date from 20 replaced sequences"
Warning in file(con, "r") :
  cannot open: HTTP status was '502 Bad Gateway'
Error in file(con, "r") : cannot open the connection
Calls: ncbiRelease -> ncbiRelease -> readLines -> file
Execution halted

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

* DONE (genomes)

name	user	system	elapsed
complete	0.083	0.011	0.094
doublingTime	0.394	0.020	0.417
enaExperiment	3.046	0.028	7.556
enaFiles	0.013	0.001	0.740
enaProject	0	0	0
enaSRA	1.887	0.011	3.539
enaStudy	2.192	0.015	5.182
enaSubmission	0.007	0.001	0.344
enaTaxonomy	0.022	0.003	2.631
genomes-lines	0.437	0.033	0.478
genomes-plot	0.367	0.025	0.393
genomes-print	0.196	0.011	0.213
genomes-subset	0.191	0.009	0.202
genomes-summary	0.034	0.002	0.035
genomes-update	0.003	0.001	0.003
genomes	0.378	0.034	0.415
genus	0.402	0.011	0.418
image2	0.406	0.020	0.428
lenvs	0.035	0.003	0.039
leuks	0.175	0.007	0.181
like	0.313	0.016	0.332
lproks	0.588	0.058	0.652
ncbiGenome	0.000	0.000	0.001
ncbiInfo	0.095	0.005	0.686
ncbiNucleotide	0.584	0.009	3.331
ncbiProject	1.167	0.017	2.359
ncbiPubmed	0.280	0.010	1.156