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

[Duncan Murdoch]

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