R devel - Aug 2010 - Does anyone use Sweave (RweaveLatex) option "expand=FALSE"?

I am trying to improve the error reporting in Sweave documents, so that 
if you have a syntax error in a code chunk, it will tell you which line 
of your input file contained the error.

For example, currently you get this:

Error:  chunk 1 (label=named)
Error in parse(text = chunk) : unexpected symbol in "x <- foo bar"
Execution halted

and I'd like errors to be more like this:

Error:  chunk 1 (label=named)
Error in parse(text = chunk, srcfile = srcfile) :
  test.Rnw:9:10: unexpected symbol
9: x <- foo bar
            ^
Execution halted

It turns out that this requires changes that make the "expand=FALSE" 
option quite hard to implement.  Is anyone using it?  For those who 
don't know it, "expand=FALSE" means that a code chunk like

<<echo=TRUE, keep.source=TRUE,expand=FALSE>>z <- 3
<<named>>
@

will be displayed as

 > z <- 3
 > <<named>>

rather than expanding the named chunk.  I'd like to drop the option, so 
that the default behaviour (which has always been equivalent to "expand 
= TRUE") would be the only behaviour.

Duncan Murdoch

On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote:
> I am trying to improve the error reporting in Sweave documents, so that if
you have a syntax error in a code chunk, it will tell you which line of your
input file contained the error.
> 
> For example, currently you get this:
> 
> Error:  chunk 1 (label=named)
> Error in parse(text = chunk) : unexpected symbol in "x <- foo
bar"
> Execution halted
> 
> and I'd like errors to be more like this:
> 
> Error:  chunk 1 (label=named)
> Error in parse(text = chunk, srcfile = srcfile) :
> test.Rnw:9:10: unexpected symbol
> 9: x <- foo bar
>           ^
> Execution halted
> 
> It turns out that this requires changes that make the
"expand=FALSE" option quite hard to implement.  Is anyone using it? 
For those who don't know it, "expand=FALSE" means that a code
chunk like
> 
> <<echo=TRUE, keep.source=TRUE,expand=FALSE>>> z <- 3
> <<named>>
> @
> 
> will be displayed as
> 
> > z <- 3
> > <<named>>
> 
> rather than expanding the named chunk.  I'd like to drop the option, so
that the default behaviour (which has always been equivalent to "expand =
TRUE") would be the only behaviour.
> 
> Duncan Murdoch

I don't. So 1 "go ahead and drop it" vote...

You may want to post this to R-Help though Duncan, as I suspect there may be
more Sweave users there than here...

Thanks and regards,

Marc Schwartz

I never used it.

I got curious, though. What would be a situation that benefits of this option?

Maybe a use case could be found by "brute force" (grep all .Rnw files
on CRAN
for the option?

Claudia

-- 
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Universit? degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste

phone: +39 0 40 5 58-37 68
email: cbeleites at units.it

On 19/08/2010 4:29 PM, Claudia Beleites wrote:
> I never used it.
>
> I got curious, though. What would be a situation that benefits of this
option?
>   
When I put it in, I thought it would be for people who were writing 
about Sweave.

Duncan Murdoch
> Maybe a use case could be found by "brute force" (grep all .Rnw
files on CRAN
> for the option?
>
> Claudia
>
>

Thank you Duncan, for expanding Sweave functionality,
notably considering error handling.

Related to that is the topic of handling warning messages.

In a course on "using R" (for beginners),
I would really like to show warnings that code chunks produce.
Currently, the warnings are printed to the console when I run
 'R CMD Sweave ..' and do not appear in the resulting *.tex file.

Of course   ---   fortune("Yoda")   ---
I can always fudge what I want,
but it would be quite desirable to have simple Sweave option
which would deal with warnings()  
{ and maybe message(), stop(), and general exception handling; 
  but for all practical purposes, it's the warnings that I'd
  like to be handled automatically.}

Martin Maechler, ETH Zurich

Duncan,
  I use noweb for my R source code on the more complex projects (see the
coxme package).  I currently have my own "noweb.R" functions to do the
work, but the overlap is so great with Sweave that I have hopes that
they will one day merge.  

A note on <<abc>> recursion: for documentation this is very well
designed; it's better than a macro or a function would be.  And of
course, documentation of code is what the system was designed for.

And a general query: I currently have the .Rnw source files in the
inst/noweb directory.  Do people have a better suggestion?  Remember
these .Rnw files are the source of my .R files and of document
explaining the code, not the source of vignettes or manual pages.

Terry Therneau