R help - Dec 2002 - Sweave & xtable

I'm trying to get Sweave running for automatic report generation, and 
it seems to run fine when just using verbatim output. However, I've ran 
into a problem with xtable. I would like to print the following matrix 
using xtable:

 > dim(counts)
[1] 19 15

All columns are filled with real/integer numbers > 0 and < 1000. Just 
typing xtable(counts) gives correct LaTeX output, but running Sweave on:

<<results=tex>>library(xtable)
xtable(counts)
@

Generates truncated TeX output:

% latex table generated in R 1.6.1 by xtable 1.0-10 package
% Fri Dec 20 14:50:08 2002
\begin{table}
[...]
5 & 105.00 & 400.00 & 0.00 & 0.00 & 0.00 & 0.00 &
1000.00 & 542.00 &
181.00 & 858.00 & 4
62.00 & 103.00 & 744.00 & 449.00 & 93.00 \\
6 & 201.00 & 400.00 & 0.00 &

xtable(counts[1:4,]) does work. Do I have to flush the output of 
xtables in some way? Or is my table just too large?

  - Hedderik.

>>>>> "hedderik" == Hedderik van Rijn <hedderik at
cmu.edu> writes:
    hedderik> I'm trying to get Sweave running for automatic report
generation, and
    hedderik> it seems to run fine when just using verbatim output. However,
I've
    hedderik> ran into a problem with xtable. I would like to print the
following
    hedderik> matrix using xtable:

I've had problems with large matrices, but never got around to
figuring out why (the cheap hack solution was to split matrices and
present in different tables).  

(matrices representing components of a model, not raw data, so it made
some sense, but wasn't optimal).

i.e. I think it might be a bug.

best,
-tony

-- 
A.J. Rossini				Rsrch. Asst. Prof. of Biostatistics
U. of Washington Biostatistics		rossini at u.washington.edu	
FHCRC/SCHARP/HIV Vaccine Trials Net	rossini at scharp.org
-------------- http://software.biostat.washington.edu/ ----------------
FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email
UW:   Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX
(my tuesday/wednesday/friday locations are completely unpredictable.)

> I'm trying to get Sweave running for automatic report generation, and 
> it seems to run fine when just using verbatim output. However, I've 
> ran into a problem with xtable.
A quick solution (as long as the table is not too wide) is to include 
the following code after library(xtable), replacing the original 
print.string

print.string <- function(x,...) {
   
lapply(strsplit(x$text,"\n")[[1]],cat,"\n",file=x$file,append=x$append)
   return(invisible())
}

The problem seems to be that textConnection() (used in the Sweave code) 
is not able to process the long strings that sometimes get sink'ed to 
it. When sending a string directly to it, a warning is triggered:

## Error/truncation with warning:
con <- textConnection("output","w");
sink(file=con);
paste(rep("123456789!",1000),collapse="");
## Warning message:
## line truncated in output text connection
sink()
rm(last.warning)

However, when a long string is send to textConnection via xtable, no 
warning is shown:

## Error/truncation without warning:
library("xtable")
con <- textConnection("output","w")
sink(file=con)
xtable(matrix(rnorm(1000),100))
sink()
## print(output) would show the truncated LaTeX table, warnings() 
doesn't show any warning

I'm not sure whether textConnection or xtable should be blamed, but 
changing the single cat() with the lapply/strsplit/cat combination in 
print.string solved the/my problem.

If the truncation of long strings is official/known behavior of 
textConnection, the following text in textConnection's help page might 
need some revision, i.e., some more explicit statement that long 
strings might get truncated. (And, maybe also a definition of what a 
"completed line of output" is, i.e., ending in a "\n".)

      An output text connection is opened and creates an R character
      vector of the given name in the user's workspace.  This object
      will at all times hold the completed lines of output to the
      connection, and `isIncomplete' will indicate if there is an
      incomplete final line.  Closing the connection will output the
      final line, complete or not.

   - Hedderik.

P.S. I've seen a lot of bus errors and segmentation faults while trying 
to find the cause of the problem. If anyone is interested, I can try to 
see if I can reproduce those. I'm using:

R : Copyright 2002, The R Development Core Team
Version 1.6.1  (2002-11-01)

% latex table generated in R 1.6.1 by xtable 1.0-11 package

This should be fixed in R-patched and R-devel (and has been since
Saturday).  Certainly it has gone away for me.

On Mon, 23 Dec 2002, Hedderik van Rijn wrote:
> >>>
cat(paste(rep("123456789!",1000),collapse=""))
> >> Program received signal SIGSEGV, Segmentation fault.
> >> 0x4207a4cb in strlen () from /lib/i686/libc.so.6
> >>
> >> (The cat(...) call being obtained with up-arrow command recall)
> >
> > To be precise, it happens *next* time I press "up"
>
> This is the same behavior I encountered. The first time _always_ goes
> fine, the next time (also by pressing "up", "enter")
sometimes(?)
> results in a segv and sometimes in a bus error. (Using R 1.6.1, Mac OS
> X, latest OS X update, 10.2.3? and just released fink installed.)
>
> As I was not sure if I could replicate it always, I only referred to it
> in a "P.S." in the second email I sent on this topic.
>
>   - Hedderik.
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595