[R] Error in Sweave but not underlying script

[Duncan Murdoch]

On 19/11/2012 3:27 PM, Bush, Daniel P. DPI wrote:
> No, that did not resolve the issue, but thanks for the suggestion.

Here's another possibility:  your Sweave session may not be setting the 
same option defaults in startup code as your regular session. This one 
just bit me:  I normally work with options(stringsAsFactors = FALSE), 
because I don't like to have strings automatically converted to 
factors.  However, this option wasn't set when running Sweave externally.

Duncan Murdoch

>
> Daniel Bush | School Finance Consultant
> School Financial Services | Wis. Dept. of Public Instruction
> daniel.bush -at- dpi.wi.gov | 608-267-9212
>
>
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
> Sent: Friday, November 16, 2012 1:51 PM
> To: Bush, Daniel P. DPI
> Cc: 'r-help at r-project.org'
> Subject: Re: [R] Error in Sweave but not underlying script
>
> On 16/11/2012 2:26 PM, Bush, Daniel P. DPI wrote:
> > I'm trying to use Sweave to create a dynamic report of a variety of financial data checks. I have an .R code file to pull the data from a database, manipulate and filter it, and create individual data frames for each test. My Sweave .RNW document then calls that file with source() to generate the data for the report. The .R file works fine on its own, but when I run it from within the Sweave document I get the following error message:
> >
> > Error in .subset(x, j) : only 0's may be mixed with negative
> > subscripts
> >
> > Again, the .R code works perfectly well on its own--I only get the error when calling it through Sweave. Is there some quirk to Sweave that certain functions don't work properly?
>
> No, it's a pretty standard evaluation environment.  However,  it may be running R without some functions that exist in your workspace when you source the script within an R session.  It's also possible (but doesn't seem likely) that RStudio is causing some problems; you could try running "R CMD Sweave yourdoc.Rnw" from the command line, outside of Rstudio, to see if that makes a difference.
>
> Duncan Murdoch
> >
> > I am using the built-in Sweave function within RStudio 0.97.168.
> >
> > DB
> >
> > Daniel Bush
> > School Finance Consultant
> > School Financial Services
> > Wisconsin Department of Public Instruction PO Box 7841 | Madison, WI
> > 53707-7841 daniel.bush -at- dpi.wi.gov | sfs.dpi.wi.gov
> > Ph: 608-267-9212 | Fax: 608-266-2840
> >
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>