[BioC] EBImage_2.6.0/R2.8.1 installation problems

[Gregoire Pau]

Hi Bernd,

First, I would suggest you to switch to the latest Bioconductor release 
2.4, which contains EBImage 3.0.0 (also available at 
http://bioconductor.org/packages/2.4/bioc/html/EBImage.html). EBImage 
3.0.0 is a major release which fixes a lot of speed/bug/design issues.

Reading/displaying an image is easy:
 > library(EBImage)
 > f = system.file("images","lena.gif", package="EBImage")
 > lena = readImage(f)
 > display(lena)

EBImage relies on ImageMagick to read images, which itself relies on 
libtiff to decipher the TIFF format. Some TIFF images can contain 
private sections, undefined in the TIFF 6.0 specification, causing 
troubles to libtiff when reading (these sections are sometimes 
deliberately used to prevent file exchange). Please check first if you 
can display the images with ImageMagick 'display' command. If not, I 
would suggest to either update your libtiff library, or to save your 
images or convert them using the software provided with your microscope 
into a more portable lossless format (PNG, BMP, TGA...).

Best regards,

Greg
---
Gregoire Pau
EMBL Research officer
http://www.ebi.ac.uk/~gpau/

Bernd Jagla wrote:
> Hi,
> 
>  
> 
> I want to use the EBImage package but when trying to access/display an image
> I get the following error message.
> 
> EBImage has never worked and this is the first time I am trying to use this
> package.
> 
> Please let me know what else I can try to make it work?
> 
>  
> 
>  
> 
> Here is the R output:
> 
>  
> 
> R version 2.8.1 (2008-12-22)
> 
> Copyright (C) 2008 The R Foundation for Statistical Computing
> 
> ISBN 3-900051-07-0
> 
>  
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> 
> You are welcome to redistribute it under certain conditions.
> 
> Type 'license()' or 'licence()' for distribution details.
> 
>  
> 
>   Natural language support but running in an English locale
> 
>  
> 
> R is a collaborative project with many contributors.
> 
> Type 'contributors()' for more information and
> 
> 'citation()' on how to cite R or R packages in publications.
> 
>  
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 
> 'help.start()' for an HTML browser interface to help.
> 
> Type 'q()' to quit R.
> 
>  
> 
> [Previously saved workspace restored]
> 
>  
> 
>> library(EBImage)
> 
>> f=system.file("images","lena.gif", package="EBImage")
> 
>> lena=readImage(f)
> 
> Warning message:
> 
> In .DoCall("lib_readImages", as.character(files), as.integer(colormode)) :
> 
>   requested image not found or could not be loaded
> 
>  
> 
> additional information:
> 
>> sessionInfo()
> 
> R version 2.8.1 (2008-12-22) 
> 
> i386-pc-mingw32 
> 
>  
> 
> locale:
> 
> 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     
> 
>  
> 
> other attached packages:
> 
> [1] EBImage_2.6.0
> 
> 
>  
> 
> Gtk information:
> 
>  
> 
> pkg-config --cflags gtk+-2.0
> 
> -mms-bitfields -Ic:/gtk/include/gtk-2.0 -Ic:/gtk/lib/gtk-2.0/include
> -Ic:/gtk/include/atk-1.0 -Ic:/gtk/include/cairo -Ic:/gtk/include/p
> 
> ango-1.0 -Ic:/gtk/include/glib-2.0 -Ic:/gtk/lib/glib-2.0/include
> -Ic:/gtk/include/libpng12
> 
>  
> 
> (GTK+-bundle2.16.0-20090317_win32)
> 
>  
> 
> ImageMagick:
> 
> ImageMagick 6.5.1 Q16 (dll version)
> 
>  
> 
> When trying to open some tif files I get the following error message:
> 
> IMDisplayDoc function (DoReadImage) reported a warning.
> 
> Imdisplay.exe: Compression algorithm does not support random access. (.)
> tiff.c/TIFFErrors/324
> 
> Gifs, miff, PNG I can open.
> 
>  
> 
> But eventually I am actually interested in opening TIFF files .
> 
>  
> 
>  
> 
> Thanks for your kind help,
> 
>  
> 
>  
> 
> Bernd
> 
>  
> 
>  
> 
> 
> 
> 
> 
> Bernd Jagla
> Bioinformatician 
> 
> Institute Pasteur
> Plate-forme puces a ADN
> Genopole / Institut Pasteur
> 28 rue du Docteur Roux
> 75724 Paris Cedex 15
> France 
> 
> 
>  <mailto:bernd.jagla at pasteur.fr> bernd.jagla at pasteur.fr 
> 
> 
> tel: 
> 
>  
> <http://www.plaxo.com/click_to_call?lang=en&src=jj_signature&To=%2B33+%280%2
> 9+140+61+35+13&Email=berndjagla at yahoo.com> +33 (0) 140 61 35 13 
> 
>  
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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