[BioC] EBImage problem - requested image not found or could not be loaded

[Gregoire Pau]

Hi Paolo,

Your example is about loading the GIF image located at:
http://soap.genome.jp/tmp/mark_pathway_www3_api5320/eco00260.gif

It works fine on my system (using the same R and EBImage). The function 
readImage of EBImage relies on ImageMagick to load images. ImageMagick 
relies on libxml2 to get URL streams.

Did you have an Internet access when running your example ? If yes, 
could you check if you can first download the GIF image (using 
download.file() in R) and then read it with readImage ? If not, it looks 
like that your ImageMagick library doesn't support URL streams (it's 
really unlikely but...). Does the following example work on your 
terminal 'display 
http://soap.genome.jp/tmp/mark_pathway_www3_api5320/eco00260.gif ' ?

Did you build ImageMagick yourself ? Do you have libxml2 installed
(type in a terminal 'xml2-config --version') ? Is the XML capability OK 
at the end of the configure step ?

On most Linux distributions (Ubuntu, Debian, Fedora, CentOS), you don't 
have to care about these things because ImageMagick comes with all its 
external features (libXML, libTIFF, SVG, gs...) enabled. But I don't 
know for Gentoo. I would suggest you to try to check the presence of 
libxml2 and try to reinstall ImageMagick and to check the configure 
options.

Best regards,

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

Paolo Sonego wrote:
> Dear all,
> Solved one problem and got another :'(
> I'm trying to use EBImage to read a gif image at a specific url.
> 
> My commands:
> 
>  > library(KEGGSOAP)
>  > url.gif <- color.pathway.by.objects("path:eco00260",
> +                              c("eco:b0002", "eco:c00263"),
> +                              c("#ff0000", "#00ff00"), c("#ffff00", 
> "yellow"))
> 
>  > library(EBImage)
>  > img <- readImage (url.gif)
> Warning message:
> In readImage(url.gif) : requested image not found or could not be loaded
>  > img
> NULL
>  >
> 
> ----------------------------
> My R session info:
>  > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-pc-linux-gnu
> 
> locale:
> C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base   
> other attached packages:
> [1] EBImage_3.0.0   abind_1.1-0     KEGGSOAP_1.18.0 fortunes_1.3-6
> 
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 SSOAP_0.4-6  XML_2.3-0    tools_2.9.0
> 
> ------------------------------
> 
> My system information:
> 
> uname -a
> 
> Linux 2.6.25-gentoo-r7 #2 SMP Wed Nov 5 17:56:30 CET 2008 x86_64 
> Intel(R) Xeon(TM) CPU 3.40GHz GenuineIntel GNU/Linux
> 
> gtk+  2.14.7
> imagemagick  6.4.8.3
> ------------------------------
> 
> 
> Any help is highly appreciated!
> 
> Regards,
> Paolo
> 
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