Error in pdf(file = iparams$output.plot.file, width = 5, height = 5) : cannot open file 'file.sorted.pdf'

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Hi,

I have been using PPQT for .bam files to obtain the fragmentsize of the reads. 
It usually works fine, however, for some files I get the following error:

Error in pdf(file = iparams$output.plot.file, width = 5, height = 5) :
  cannot open file 'file.sorted.pdf'
Execution halted

When this happens I still get an output file, however, col3 contains only 1 
value instead of the usual 3.

This is my input:

Rscript run_spp.R -c=file.sorted.bam -savp -out=file_PPQT.csv

The files that give this error are usually mapped with bwa (and contain 
duplicate reads and reads mapping to repeat regions), while files that do not 
produce this error are mapped with ELAND (and contain duplicate reads but not 
read mapping to repeat regions).

How can I fix this error, and can I trust the output data?

Thank you for your help,

Saartje (Nijmegen, The Netherlands)

Original issue reported on code.google.com by Saartje....@gmail.com on 15 Mar 2013 at 8:09