[R] Sweave, cacheSweave, and data frame

[Andreas Borg]

It's been a while since this thread appeared, but I had the same problem 
and don't want to keep the solution for myself.

A small, reproducible example:

<<cache=true>>=
a=1
@

<<>>=
a+1
@

Compiling with cacheSweave gives an error:

 > library(cacheSweave)
Lade nötiges Paket: filehash
filehash: Simple key-value database (2.0-1 2008-12-19)
Lade nötiges Paket: stashR
A Set of Tools for Administering SHared Repositories (0.3-3 2009-03-26)
 > Sweave("cacheSweaveExample.rnw", driver=cacheSweaveDriver)
Writing to file cacheSweaveExample.tex
Processing code chunks ...
 1 : echo term verbatim
Fehler in data.frame(chunk = options$label, chunkprefix = chunkprefix,  :
  arguments imply differing number of rows: 0, 1

The solution is to use named code chunks as in this corrected example:

<<a, cache=true>>=
a=1
@

<<b>>=
a+1
@

The problem is that the cacheSweave driver tries to store the label of a 
code chunk, along with other information, in a data frame. If there is 
no label, the corresponding variable is NULL which gives an error.

I don't know if this is a bug or intended. I think it is more safe this 
way than to rely on some automatic labelling. Anyway, there should be a 
note in the documentation.


> Shige Song
> Sat, 25 Jul 2009 20:07:47 -0700
>
> Dear All,
>
> I have been using Sweave (mainly via the Sweave.sh script) and really like
> it. I am working a paper (using Sweave, of course) which includes several
> time-consuming computations, and it gets tedious to re-compile the whoel
> thing every time I made changes. Then I discover the "cacheSweave" package,
> which seems the right solution to my problem. I only have on problem. Here
> is what I did:
>
> ----------------------------------------------
> <<results=hide,echo=false>>=
> library(foreign)
> library(Zelig)
> library(memisc)
> options(digits=4)
> @
>
> <<echo=false>>=
> d <- read.dta("~/project/abortion/data/data_transition_wide.dta")
> @
>
> ...
>
> ----------------------------------------------
>
> It can be compiled using "Sweave.sh foo.Rnw", but when I tried "Sweave.sh -c
> foo.Rnw", I got error message:
>  "...Processing code chunks ...
> 1 : term hide
> Error in data.frame(chunk = options$label, chunkprefix = chunkprefix,  :
>  arguments imply differing number of rows: 0, 1"
>
> I thought it might be an imcompatibiltiy problem between the cacheSweave and
> the foreign packages, but the problem was still there when I tried to read
> the data in using "read.table" function.
>
> Any ideas? Many thanks.
>
> Best,
> Shige
>   

-- 
Andreas Borg
Medizinische Informatik

UNIVERSITÄTSMEDIZIN
der Johannes Gutenberg-Universität
Institut für Medizinische Biometrie, Epidemiologie und Informatik
Obere Zahlbacher Straße 69, 55131 Mainz
www.imbei.uni-mainz.de

Telefon +49 (0) 6131 175062
E-Mail: borg at imbei.uni-mainz.de

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