[Rd] Syntax Error in Rcmd check on Windows

[Duncan Murdoch]

On 10/31/2006 8:38 AM, Michael Hoehle wrote:
> Dear R-developers,
> 
> I am currently developing an R package called RLadyBug. When
> developing under Linux "R CMD check ." works fine without a warning.
> However, when I do "Rcmd check ." under Windows (version 2.4.0 and
> earlier)  I get a „syntax error" when checking the examples.
> 
> This puzzles me somewhat, because a manual source("RLadyBug-Ex.R") on
> Windows works fine. On the other hand, a "Rterm.exe --no-save <
> RLadyBug-Ex.R" in a command shell under Windows reproduces the error.
> My first guess was that the very long line was causing the problem,
> but when I open RLadyBug-Ex.R in Emacs, change the coding system from
> "undecided-dos" to "undecided-unix" and save the file "Rterm.exe
> --no-save < RLadyBug-Ex.R" works fine....
> 
> Does anybody has an idea what is causing the error and how to fix this?

No. Could you send me the RLadyBug-Ex.R file?  I'd like to get an exact 
copy of what you have, so please put it in a .zip or other archive.  If 
you use .zip, you'll need to rename it when mailing (or just put it on a 
web page somewhere), because our mail server doesn't accept emailed .zip 
files.

Duncan Murdoch

> 
> Best regards,
> 
> Michael Höhle
> 
> --
> 
> ---
> * checking for working latex ... OK
> * using log directory 'z:/Transmission/RLadyBug/..Rcheck'
> * using R version 2.4.0 (2006-10-03)
> * checking for file './DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'RLadyBug' version '0.4-1'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'RLadyBug' 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 syntax errors ... OK
> * checking R files for non-ASCII characters ... 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 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 cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * creating RLadyBug-Ex.R ... OK
> * checking examples ... ERROR
> Running examples in 'RLadyBug-Ex.R' failed.
> The error most likely occurred in:
> 
>> ### * LBExperiment-class
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: LBExperiment-class
>> ### Title: Class "LBExperiment"
>> ### Aliases: LBExperiment-class show,LBExperiment-method
>> ###   plot,LBExperiment-method plot,LBExperiment,missing-method
>> ###   summary,LBExperiment-method data2events,LBExperiment-method
>> ###   data2events
>> ### Keywords: classes
>>
>> ### ** Examples
>>
>> sim.layout <- new( "LBLayout", S0=matrix( c( 13, rep( 14, 7 ) ), ncol=4 ),
> +                   E0=matrix( c(  1, rep(  0, 7 ) ), ncol=4 ) )
>> sim.opts <- new( "LBOptions", seed=2006,
> +                             LBmodel=c( "gamma", "gamma", "gamma", FALSE ),
> +                             ignoreData=c( FALSE, FALSE, FALSE ),
> +                             initBeta =list( init=0.125,
> +                                         gamma=0.001, delta=0.001 ),
> +                             initBetaN=list( init=0.018,
> +                                         gamma=0.001, delta=0.001 ),
> +                             initIncu=list( asis=FALSE, const=FALSE,
> +                                     g=6.697, g.gamma=0.001, g.delta=0.001,
> +                                     d=0.84, d.gamma=0.001,d.delta=0.001 ),
> +                             initInf=list( 1.772, 0.001, 0.001,
> 0.123, 0.001, 0.001 ),
> +                             initDia=list( 149.126, 0.001, 0.001,
> +                                     8.737, 0.001, 0.001 ) )
> Error: syntax error in:
> "a=list( 149.126, 0.001, 0.001,
> "                                   8.737, 0.001, 0.001 ) )
> Execution halted

Is there a closing parenthesis not shown?  Because they don't balance in 
that expression.