From ripley at stats.ox.ac.uk  Tue Mar 11 21:35:55 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 11 Mar 2008 20:35:55 +0000 (GMT)
Subject: [Rd] R-console vs. bash console (execution halted)
In-Reply-To: <A0C7AADAEF32A64696B51EC0F31A90E303E3CEF0@EX4.d.ethz.ch>
References: <A0C7AADAEF32A64696B51EC0F31A90E303E3CEF0@EX4.d.ethz.ch>
Message-ID: <alpine.LFD.1.00.0803112031240.15769@gannet.stats.ox.ac.uk>

Your first use is non-interactive.  I have no idea what

R CMD source("/data/myscript.R")

is supposed to do (it does not work for me), but source() when run in RGui 
is interactive.

See ?options and in particular 'error' and the reference to ?stop for the 
different ways errors are handled in interactive and non-interactive use.



On Tue, 11 Mar 2008, Lienert  Christophe wrote:

> Dear Everyone,
> I am using R 2.6.2 on my Redhat AS4. I installed the RPM offered on the cran website. I would like to use R from my bash console with the following command:
>
> /path/to/R --vanilla --slave --args < /data/myscript.R
>
> this script invokes a range of functions and tools, among others to process a bunch of raster images in a loop using GDAL. The thing is that releasing this command in the bash results in the following error
>
>
> Error in function (handle)  :
>        GDAL Error 1: TIFFReadDirectory:/tmp/RtmpPCALnL/file265f67a6: cannot handle zero scanline size
> Calls: <Anonymous> -> .Call
> Execution halted
>
> The scripts halts, although there are more images to process. The question is why the script halts and why the script is not halted (but still "decorated" with errors) when releasing it within the R console like so
>
> R CMD source("/data/myscript.R")
>
> The result of this R CMD is shown below. Note that the script is doing what it is supposed to, despite the error it produces. The loop is completely finalized
>
> Error in function (handle)  :
>        GDAL Error 1: TIFFReadDirectory:/tmp/Rtmp6gXG5W/file67e9e074: cannot handle zero scanline size
> [1] "/data/someimg1.tiff"
> Error in function (handle)  :
>        GDAL Error 1: TIFFReadDirectory:/tmp/Rtmp6gXG5W/file21e4ef74: cannot handle zero scanline size
> [1] "/data/someimg2.tiff"
> Error in function (handle)  :
>        GDAL Error 1: TIFFReadDirectory:/tmp/Rtmp6gXG5W/file67e9e074: cannot handle zero scanline size
> [1] "/data/someimg3.tiff"
>
> etc.
>
> Obviously, the tmp directory is being deleted before the stored image in it can be used. Does anybody know what to consider or provide when working in a external console like bash and/or does anybody know about such halted executions when working with GDAL?
> Help is greatly appreciated,
>
> Ciao,
> Chris
>
> _______________________________________________
> Christophe Lienert
> ETH Zurich
> Institute of Cartography
> Wolfgang-Pauli-Str. 15
> HIL G 13.3
> CH-8093 Zurich
> SWITZERLAND
>
> Fon: +41-44-6333036
> Fax: +41-44-6331153
> www.karto.ethz.ch
> lienert at karto.baug.ethz.ch
> <mailto:lienert at karto.baug.ethz.ch>
>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
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



[Rd] R-console vs. bash console (execution halted)
Prof Brian Ripley