* 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)