Package: rols

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.2.0.tar.gz

StartedAt: 2013-05-01 10:31:05 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:32:40 -0700 (Wed, 01 May 2013)

EllapsedTime: 94.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: rols.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rols.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '1.2.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'rols' can be installed ... [9s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
Found the following possibly unsafe calls:
File 'rols/R/queries.R':
  unlockBinding("ontologies", .rolsEnv)
* 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 installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'rols-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CVParam-class
> ### Title: Class '"CVParam"'
> ### Aliases: CVParam-class CVParam coerce,CVParam,character-method
> ###   show,CVParam-method rep,CVParam-method as.character.CVParam
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## a user param
> CVParam(name = "A user param", value = "the value")
[, , A user param, the value] 
> ## a CVParam from PSI's Mass Spectrometry ontology
> term("PSI:1000073", "PSI")
Error in match.arg(ontologyName, ontologyNames()) : 
  'arg' should be one of "LSM", "TADS", "FBsp", "FIX", "HOM", "SPD", "HP", "RO", "MOD", "BTO", "MFO", "TTO", "WBls", "BFO", "APO", "MAT", "NEWT", "MI", "FAO", "TAIR", "IDO", "EMAP", "PRO", "AAO", "OBO_REL", "ZFA", "MA", "TRANS", "XAO", "PATO", "TGMA", "PRIDE", "UO", "REX", "CARO", "TAO", "SEP", "MP", "EV", "HAO", "FBdv", "MS", "GRO", "EO", "EDAM", "PAR", "IMR", "PW", "IEV", "MIAA", "ECO", "ENVO", "BS", "CCO", "TO", "FBcv", "DDANAT", "MIRO", "FYPO", "SYMP", "WBPhenotype", "CHEBI", "GAZ", "DOID", "BSPO", "ZDB", "WBbt", "FBbi", "ATO", "FBbt", "SO", "EHDA", "FMA", "PM", "ZEA", "PO", "SBO", "EFO", "UBERON", "TAXRANK", "GO", "ENA", "MPATH", "CL"
Calls: term -> match.arg
Execution halted

* installing *source* package 'rols' ...
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
* DONE (rols)

name	user	system	elapsed