EBImage installation
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Bernd Jagla ▴ 40
@bernd-jagla-3411
Last seen 18 months ago
Hi, I am trying to install EBImage (now on a MacPro) I have ImageMagick 6.5.1-0 installed (using MacPort) and gtk2 (2.16.1, also using MacPort). When I install EBImage everything is OK. But when executing / loading the library it complains that libraries are not available. I then look for those libraries and symbolically link them to the directory where they are "supposed" to be. This worked reasonably well (I actually think it should be working out of the box). Now I am stuck with ImageMagick that should be in /usr/local/lib/libMagick.10.dylib. I couldn't find this file on my computer but I guess it should be there because the description of the MacPort package says that the libraries are installed as well. And I also tried to recompile from source: Here I don't get passed the ./configure script. There are no error message and no Makefile is created. I don't know what is going wrong here. Thanks for your comments and help. Sorry for my ignorance. Best, Bernd [[alternative HTML version deleted]]
EBImage EBImage • 821 views
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Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.7 years ago
Hi Bernd, If you have the libraries ImageMagick (6.5.1-0) and gtk2 (2.16.1) installed with MacPort then the following shell commands, - 'display --version' - 'gtk-demo' should work (testing ImageMagick and GTK+). Just download the *source* package of EBImage here: http://bioconductor.org/packages/2.4/bioc/html/EBImage.html and install it using 'R CMD INSTALL EBImage_3.0.0.tar.gz'. That's it and EBImage should work fine. I suspect you did something wrong because MacPort installs libraries in /opt/local/lib (and not in /usr/lib) so maybe you were trying to install the Mac binary package of EBImage which seems to use /usr/local/lib/libMagick.10.dylib. But the name of the ImageMagick library has changed since... (it is now called libMagickCore, explaining why you can't find it on your system). If it doesn't work, could you please give me all your details with sessioInfo() and the output of the following commands: - 'otool -L src/EBImage.so' - 'Magick-config --libs' - 'pkg-config gtk+-2.0 --libs' Best regards, Greg --- Gregoire Pau EMBL Research Officer http://www.ebi.ac.uk/~gpau/ Bernd Jagla wrote: > Hi, > > > > I am trying to install EBImage (now on a MacPro) > > > > I have ImageMagick 6.5.1-0 installed (using MacPort) and gtk2 (2.16.1, also > using MacPort). > > > > When I install EBImage everything is OK. But when executing / loading the > library it complains that libraries are not available. I then look for those > libraries and symbolically link them to the directory where they are > "supposed" to be. This worked reasonably well (I actually think it should be > working out of the box). Now I am stuck with ImageMagick that should be in > /usr/local/lib/libMagick.10.dylib. > > I couldn't find this file on my computer but I guess it should be there > because the description of the MacPort package says that the libraries are > installed as well. > > > > And I also tried to recompile from source: Here I don't get passed the > ./configure script. There are no error message and no Makefile is created. I > don't know what is going wrong here. > > > > Thanks for your comments and help. Sorry for my ignorance. > > > > Best, > > > > Bernd > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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Hi, Thanks I was able to compile from sources now and everythings works fine. I just get the following message: > library(EBImage) Le chargement a ncessit le package : abind Xlib: extension "RANDR" missing on display "/tmp/launch-1igmhB/:0". By the way, do you know how to change from French to English? Thanks, Bernd -----Original Message----- From: Gregoire Pau [mailto:gregoire.pau@embl.de] Sent: Wednesday, April 29, 2009 4:37 PM To: Bernd Jagla Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] EBImage installation Hi Bernd, If you have the libraries ImageMagick (6.5.1-0) and gtk2 (2.16.1) installed with MacPort then the following shell commands, - 'display --version' - 'gtk-demo' should work (testing ImageMagick and GTK+). Just download the *source* package of EBImage here: http://bioconductor.org/packages/2.4/bioc/html/EBImage.html and install it using 'R CMD INSTALL EBImage_3.0.0.tar.gz'. That's it and EBImage should work fine. I suspect you did something wrong because MacPort installs libraries in /opt/local/lib (and not in /usr/lib) so maybe you were trying to install the Mac binary package of EBImage which seems to use /usr/local/lib/libMagick.10.dylib. But the name of the ImageMagick library has changed since... (it is now called libMagickCore, explaining why you can't find it on your system). If it doesn't work, could you please give me all your details with sessioInfo() and the output of the following commands: - 'otool -L src/EBImage.so' - 'Magick-config --libs' - 'pkg-config gtk+-2.0 --libs' Best regards, Greg --- Gregoire Pau EMBL Research Officer http://www.ebi.ac.uk/~gpau/ Bernd Jagla wrote: > Hi, > > > > I am trying to install EBImage (now on a MacPro) > > > > I have ImageMagick 6.5.1-0 installed (using MacPort) and gtk2 (2.16.1, also > using MacPort). > > > > When I install EBImage everything is OK. But when executing / loading the > library it complains that libraries are not available. I then look for those > libraries and symbolically link them to the directory where they are > "supposed" to be. This worked reasonably well (I actually think it should be > working out of the box). Now I am stuck with ImageMagick that should be in > /usr/local/lib/libMagick.10.dylib. > > I couldn't find this file on my computer but I guess it should be there > because the description of the MacPort package says that the libraries are > installed as well. > > > > And I also tried to recompile from source: Here I don't get passed the > ./configure script. There are no error message and no Makefile is created. I > don't know what is going wrong here. > > > > Thanks for your comments and help. Sorry for my ignorance. > > > > Best, > > > > Bernd > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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