Package: ChemmineR

Version: 1.6.0

Command: E:\biocbld\bbs-2.5-bioc\R\bin\R.exe CMD check --no-vignettes ChemmineR_1.6.0.tar.gz

StartedAt: 2010-04-03 04:16:10 -0700 (Sat, 03 Apr 2010)

EndedAt: 2010-04-03 04:17:02 -0700 (Sat, 03 Apr 2010)

EllapsedTime: 52.2 seconds

RetCode: 1

Status: ERROR

CheckDir: ChemmineR.Rcheck

Warnings: NA

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.5-bioc/meat/ChemmineR.Rcheck'
* using R version 2.10.1 (2009-12-14)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '1.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ChemmineR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... 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 examples ... ERROR
Running examples in 'ChemmineR-Ex.R' failed.
The error most likely occurred in:

> ### * cmp.parse1
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: cmp.parse1
> ### Title: Parsing an SDF file and calculate the descriptor for one
> ###   compound
> ### Aliases: cmp.parse1
> ### Keywords: utilities
> 
> ### ** Examples
> 
> # load an SDF file from web and parse it
> structure <- cmp.parse1(
+     "http://bioweb.ucr.edu/ChemMineV2/compound/Aurora/b32:NNQS2MBRHAZTI===/sdf")
Warning in .parse(filename) : NAs introduced by coercion
Warning in .parse(filename) : NAs introduced by coercion
Error in if (length(num_atoms) == 0 || num_atoms == 0) return(list(atoms = vector(),  : 
  missing value where TRUE/FALSE needed
Calls: cmp.parse1 -> .parse
Execution halted

* install options are ' --no-html'

* installing *source* package 'ChemmineR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (ChemmineR)