[BioC] heatmap output problems in pdf

Saroj K Mohapatra smohapat at vbi.vt.edu
Wed Mar 11 23:05:58 CET 2009

Hi Pete:

It is difficult for others to know what the problem is unless you send some code that would reproduce the error. For example, the following three lines would create a pdf document (in the working directory) with the image of a plot.

> pdf(file="temp.pdf")
> plot(1:10)
> dev.off()

I have checked; the file opens outside of R with the expected image.

You can check if you are able to run this code and create a plot. If not, send all of the following:
1. the code
2. the R outputs and 
3. output of the command sessionInfo() [look at an example below]



> sessionInfo()
R version 2.8.1 (2008-12-22) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

----- Original Message -----
From: "Pete Shepard" <peter.shepard at gmail.com>
To: bioconductor at stat.math.ethz.ch
Sent: Wednesday, March 11, 2009 5:30:25 PM GMT -05:00 US/Canada Eastern
Subject: [BioC] heatmap output problems in pdf

Dear List,

I am using heatmap to output a microarray image to a pdf file. I get an
error message when I do this:

Error: PDF file is damaged - attempting to reconstruct xref table...
Error: Couldn't find trailer dictionary
Error: Couldn't read xref table

The file opens fine in default mode "X11 I think".

1) Do people generally output to pdfs?
2) Is there a fix? If not what other formats to people output their graphics
to in order to present them?


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