[R] \Sweaveopts error

[John Maindonald]

Actually, I had until I created this file had everything on one line,
or had separate \SweaveOpts commands.

Putting everything on one line ensures that the graphics file
goes to the subdirectory snArt, but the file test1.tex is unchanged.

Note however the difference between the files test1.tex and
test.tex, irrespective of the 1 line or 2 issue.  The first of the
\SweaveOpts lines had an effect, unless I am missing something.

John.

John Maindonald             email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm

On 28/11/2010, at 12:40 PM, Duncan Murdoch wrote:

> On 27/11/2010 7:57 PM, John Maindonald wrote:
>> Actually, I spoke too soon.  The files process without obvious error,
>> but keep.source=TRUE is ignored.  I have posted small files
>> test1.Rnw and test2.Rnw that can be used to demonstrate the
>> problems at:
>>   http://wwwmaths.anu.edu.au/~johnm/r/issues/
> 
> In the test1.Rnw file, your \SweaveOpts statement spans two lines. Sweave() doesn't recognize it, so it's completely ignored.
> 
> I don't think this is new behaviour; it's a consequence of the way Sweave looks for \SweaveOpts via regular expression.
> 
> Not quite sure what's going on in the second one yet...
> 
> Duncan Murdoch
> 
>> 
>> Sweave("test1")  ## includes SweaveOpts settings
>> 
>> Sweave("test2", keep.source=TRUE)
>>                               ## SweaveOpts settings have been removed.
>> 
>> Comments do not appear in the LaTeX file that results, the code
>> is reformatted and the graph from test1 goes into the working
>> directory.
>> 
>> Notice also the NA that mysteriously appears in the second
>> line of code in output .tex file test2.tex
>> 
>> John.
>> 
>> John Maindonald             email: john.maindonald at anu.edu.au
>> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
>> Centre for Mathematics&  Its Applications, Room 1194,
>> John Dedman Mathematical Sciences Building (Building 27)
>> Australian National University, Canberra ACT 0200.
>> http://www.maths.anu.edu.au/~johnm
>> 
>> On 26/11/2010, at 4:26 PM, John Maindonald wrote:
>> 
>>> Yes, that has fixed the problem. (2010-11-24 r53659)
>>> 
>>> Thanks.
>>> 
>>> John Maindonald             email: john.maindonald at anu.edu.au
>>> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
>>> Centre for Mathematics&  Its Applications, Room 1194,
>>> John Dedman Mathematical Sciences Building (Building 27)
>>> Australian National University, Canberra ACT 0200.
>>> http://www.maths.anu.edu.au/~johnm
>>> 
>>> On 25/11/2010, at 10:56 PM, Duncan Murdoch wrote:
>>> 
>>>> On 25/11/2010 6:34 AM, John Maindonald wrote:
>>>>> I have a file 4lmetc.Rnw, intended for inclusion in a LaTeX document,
>>>>> that starts:
>>>> 
>>>> I think this may have been fixed in the patched version.  Could you give it a try to confirm?  If not, please send me a simplified version of the file, and I'll see what's going wrong.
>>>> 
>>>> Duncan Murdoch
>>>> 
>>>> 
>>>>> 
>>>>> \SweaveOpts{engine=R, keep.source=TRUE}
>>>>> \SweaveOpts{eps=FALSE, prefix.string=snArt/4lmetc}
>>>>> 
>>>>> The attempt to process the file through Sweave generates the error:
>>>>> 
>>>>>> Sweave("4lmetc")
>>>>> Writing to file 4lmetc.tex
>>>>> Processing code chunks ...
>>>>> 1 : keep.source term verbatim
>>>>> Error in file(srcfile$filename, open = "rt", encoding = encoding) :
>>>>> cannot open the connection
>>>>> In addition: Warning message:
>>>>> In file(srcfile$filename, open = "rt", encoding = encoding) :
>>>>> cannot open file '4lmetc': No such file or directory
>>>>> 
>>>>> The same file processes through Stangle() without problems.
>>>>> If I comment out the \Sweaveopts lines, there is no problem,
>>>>> except that I do not get the options that I want.
>>>>> 
>>>>> This processed fine in R-2.11.1
>>>>> 
>>>>>> sessionInfo()
>>>>> R version 2.12.0 (2010-10-15)
>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>> 
>>>>> locale:
>>>>> [1] C
>>>>> 
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  grid      methods
>>>>> [8] base
>>>>> 
>>>>> other attached packages:
>>>>> [1] lattice_0.19-13     DAAG_1.02           randomForest_4.5-36
>>>>> [4] rpart_3.1-46        MASS_7.3-8          reshape_0.8.3
>>>>> [7] plyr_1.2.1          proto_0.3-8
>>>>> 
>>>>> loaded via a namespace (and not attached):
>>>>> [1] ggplot2_0.8.8       latticeExtra_0.6-14
>>>>> 
>>>>> Is there a workaround?
>>>>> 
>>>>> John Maindonald             email: john.maindonald at anu.edu.au
>>>>> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
>>>>> Centre for Mathematics&   Its Applications, Room 1194,
>>>>> John Dedman Mathematical Sciences Building (Building 27)
>>>>> Australian National University, Canberra ACT 0200.
>>>>> http://www.maths.anu.edu.au/~johnm
>>>>> 
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>> 
>>> 
>> 
>