* using log directory 'C:/R/biocbld/1.7/build-area/buildSandbox/checkOutput/msbase.Rcheck'
* using R version 2.2.0, 2005-10-10 
* checking for file 'msbase/DESCRIPTION' ... OK
* this is package 'msbase' version '1.4.0'
* checking if this is a source package ... OK
* checking whether package 'msbase' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* creating msbase-Ex.R ... OK
* checking examples ... ERROR
Running examples in msbase-Ex.R failed.
The error most likely occurred in:

> ### * cals-methods
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: cals-methods
> ### Title: Similarity by user defined function
> ### Aliases: cals-methods cals,numeric,numeric-method
> ###   cals,Massvector,Massvector-method
> ###   cals,Massvectorlist,Massvector-method cals,Massvectorlist,NULL-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(pldata)
> pl1 <- pldata[[1]]
> pl2 <- pldata[[2]]
> cals(pl1,pl2,error=400,ppm=TRUE,msim=calssim,p=3)