EBImage problem - requested image not found or could not be loaded
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Paolo Sonego ▴ 140
@paolo-sonego-3256
Last seen 7.7 years ago
Italy
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
EBImage EBImage • 830 views
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Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.7 years ago
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Gregoire, Thanks so much! Thanks to your suggestions my admin managed to solve the problem! It seems, if I understand correctly, that under gentoo the default installation of ImageMagick doesn't include libXML support. Emerging(gentoo-lingo to mean install, i guess) the ImageMagick package with libXML support did the trick! Thanks again! Regards, Paolo Gregoire Pau ha scritto: > 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
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