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Michael Kubovy

2008-Mar-30 01:47 UTC

[R] Second & subsequent calls to function fails. Please help debug.

Dear R-helpers,

I'm running Sweave() on a file. First run:
 > Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
  1 : term hide (label=setup)
  2 : echo term verbatim (label=oatvar)
  3 : echo term verbatim (label=oatvar1)
  4 : echo term verbatim (label=oat2wt)
  5 : echo term verbatim (label=oat2wt)
  6 : echo term verbatim (label=lm)
  7 : echo term verbatim (label=diag)
  8 : echo term verbatim (label=tukey)
  9 : echo term verbatim (label=efficiency)
10 : echo term verbatim (label=wear)
11 : echo term verbatim (label=wearX)
12 : echo term verbatim (label=gyd)
Loading required package: crossdes
Loading required package: AlgDesign
Loading required package: gtools

Attaching package: 'gtools'


	The following object(s) are masked from package:faraway :

	 logit

Loading required package: MASS
13 : echo term verbatim (label=2wt)
14 : echo term verbatim (label=ablm)
15 : echo term verbatim (label=abaov)

You can now run LaTeX on '20080331.tex'
There were 42 warnings (use warnings() to see them)

Second run:
 > Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
  1 : term hide (label=setup)
  2 : echo term verbatim (label=oatvar)
  3 : echo term verbatim (label=oatvar1)
  4 : echo term verbatim (label=oat2wt)
  5 : echo term verbatim (label=oat2wt)
  6 : echo term verbatim (label=lm)
  7 : echo term verbatim (label=diag)
  8 : echo term verbatim (label=tukey)

Error:  chunk 8 (label=tukey)
Error in parse(text = x) :
   unexpected symbol in "yield ~ variety + block + preds(yield+variety 
+block+preds.sq)sq"

It failed in:

<<tukey>>require(alr3)
tukey.nonadd.test(ov.lm)
@

At that point I ran debug() on the call:
debug(tukey.nonadd.test)
tukey.nonadd.test(ov.lm)
debugging in: tukey.nonadd.test(ov.lm1)
debug: {
     envir <- environment(formula(m))
     dd <- eval(m$call$data, envir)
     subs <- eval(m$call$subset, envir)
     wgts <- eval(m$call$weights, envir)
     naa <- m$call$na.action
     dd <- data.frame(dd, preds.sq = predict(m, dd)^2)
     uf <- update.formula(formula(m$terms), ~. + preds.sq)
     environment(uf) <- environment(NULL)
     mup <- if (is.null(naa))
         lm(uf, data = dd, subset = subs, weights = wgts)
     else lm(uf, data = dd, subset = subs, weights = wgts, na.action =  
naa)
     if (mup$rank > m$rank) {
         ans <- summary(mup)$coef[, 3:4]
         ans <- ans[match("preds.sq", rownames(ans)), ]
         ans[2] <- pnorm(-abs(ans[1])) * 2
         ans
     }
     else c(NA, NA)
}
Browse[1]>
debug: envir <- environment(formula(m))
Browse[1]>
debug: dd <- eval(m$call$data, envir)
Browse[1]>
debug: subs <- eval(m$call$subset, envir)
Browse[1]>
debug: wgts <- eval(m$call$weights, envir)
Browse[1]>
debug: naa <- m$call$na.action
Browse[1]>
debug: dd <- data.frame(dd, preds.sq = predict(m, dd)^2)
Browse[1]>
debug: uf <- update.formula(formula(m$terms), ~. + preds.sq)
Browse[1]>
debug: environment(uf) <- environment(NULL)
Browse[1]>
debug: mup <- if (is.null(naa)) lm(uf, data = dd, subset = subs,  
weights = wgts) else lm(uf,
     data = dd, subset = subs, weights = wgts, na.action = naa)
Browse[1]>
Error in parse(text = x) :
   unexpected symbol in "yield ~ variety + preds(yield+variety 
+preds.sq)sq"

Advice?
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS:     P.O.Box 400400    Charlottesville, VA 22904-4400
Parcels:    Room 102        Gilmer Hall
         McCormick Road    Charlottesville, VA 22903
Office:    B011    +1-434-982-4729
Lab:        B019    +1-434-982-4751
Fax:        +1-434-982-4766
WWW:    http://www.people.virginia.edu/~mk9y/



	[[alternative HTML version deleted]]

Duncan Murdoch

2008-Mar-30 02:41 UTC

head link

[R] Second & subsequent calls to function fails. Please help debug.

On 29/03/2008 9:47 PM, Michael Kubovy wrote:> Dear R-helpers,
> 
> I'm running Sweave() on a file. First run:
>  > Sweave('20080331.Rnw')
> Writing to file 20080331.tex
> Processing code chunks ...
>   1 : term hide (label=setup)
>   2 : echo term verbatim (label=oatvar)
>   3 : echo term verbatim (label=oatvar1)
>   4 : echo term verbatim (label=oat2wt)
>   5 : echo term verbatim (label=oat2wt)
>   6 : echo term verbatim (label=lm)
>   7 : echo term verbatim (label=diag)
>   8 : echo term verbatim (label=tukey)
>   9 : echo term verbatim (label=efficiency)
> 10 : echo term verbatim (label=wear)
> 11 : echo term verbatim (label=wearX)
> 12 : echo term verbatim (label=gyd)
> Loading required package: crossdes
> Loading required package: AlgDesign
> Loading required package: gtools
> 
> Attaching package: 'gtools'
> 
> 
> 	The following object(s) are masked from package:faraway :
> 
> 	 logit
> 
> Loading required package: MASS
> 13 : echo term verbatim (label=2wt)
> 14 : echo term verbatim (label=ablm)
> 15 : echo term verbatim (label=abaov)
> 
> You can now run LaTeX on '20080331.tex'
> There were 42 warnings (use warnings() to see them)
> 
> Second run:
>  > Sweave('20080331.Rnw')
> Writing to file 20080331.tex
> Processing code chunks ...
>   1 : term hide (label=setup)
>   2 : echo term verbatim (label=oatvar)
>   3 : echo term verbatim (label=oatvar1)
>   4 : echo term verbatim (label=oat2wt)
>   5 : echo term verbatim (label=oat2wt)
>   6 : echo term verbatim (label=lm)
>   7 : echo term verbatim (label=diag)
>   8 : echo term verbatim (label=tukey)
> 
> Error:  chunk 8 (label=tukey)
> Error in parse(text = x) :
>    unexpected symbol in "yield ~ variety + block + preds(yield+variety
> +block+preds.sq)sq"
> 
> It failed in:
> 
> <<tukey>>> require(alr3)
> tukey.nonadd.test(ov.lm)
> @
> 
> At that point I ran debug() on the call:
> debug(tukey.nonadd.test)
> tukey.nonadd.test(ov.lm)
> debugging in: tukey.nonadd.test(ov.lm1)
> debug: {
>      envir <- environment(formula(m))
>      dd <- eval(m$call$data, envir)
>      subs <- eval(m$call$subset, envir)
>      wgts <- eval(m$call$weights, envir)
>      naa <- m$call$na.action
>      dd <- data.frame(dd, preds.sq = predict(m, dd)^2)
>      uf <- update.formula(formula(m$terms), ~. + preds.sq)
>      environment(uf) <- environment(NULL)
>      mup <- if (is.null(naa))
>          lm(uf, data = dd, subset = subs, weights = wgts)
>      else lm(uf, data = dd, subset = subs, weights = wgts, na.action =  
> naa)
>      if (mup$rank > m$rank) {
>          ans <- summary(mup)$coef[, 3:4]
>          ans <- ans[match("preds.sq", rownames(ans)), ]
>          ans[2] <- pnorm(-abs(ans[1])) * 2
>          ans
>      }
>      else c(NA, NA)
> }
> Browse[1]>
> debug: envir <- environment(formula(m))
> Browse[1]>
> debug: dd <- eval(m$call$data, envir)
> Browse[1]>
> debug: subs <- eval(m$call$subset, envir)
> Browse[1]>
> debug: wgts <- eval(m$call$weights, envir)
> Browse[1]>
> debug: naa <- m$call$na.action
> Browse[1]>
> debug: dd <- data.frame(dd, preds.sq = predict(m, dd)^2)
> Browse[1]>
> debug: uf <- update.formula(formula(m$terms), ~. + preds.sq)
> Browse[1]>
> debug: environment(uf) <- environment(NULL)
> Browse[1]>
> debug: mup <- if (is.null(naa)) lm(uf, data = dd, subset = subs,  
> weights = wgts) else lm(uf,
>      data = dd, subset = subs, weights = wgts, na.action = naa)
> Browse[1]>
> Error in parse(text = x) :
>    unexpected symbol in "yield ~ variety + preds(yield+variety 
> +preds.sq)sq"
> 
> Advice?
> ________
I don't see anything obvious, so I guess it's the usual advice:

Use traceback() to see what function was trying to do the parsing. 
Debug that function, and see why it was trying to parse that string.
If that doesn't make it obvious, put together a minimal reproducible 
version that others can try, and see if anyone else can spot the problem.

Duncan Murdoch

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