[BioC] EBImage package

[Dan Tenenbaum]

On Fri, Feb 17, 2012 at 7:13 AM, Jordi van Gestel <jb.jordi at gmail.com> wrote:
> Dear Mrs./Mr.,
>
>
>
> I am Jordi, PhD student at the University of Groningen (the Netherlands). I
> am working on *Bacillus subtilis* at the Molecular Genetics lab, in which
> we study the expression of some genes by using fluorescent proteins. To
> analyze the pictures that are made during the experiments I was advised to
> use the EBImage package in R (I originally used MATLAB, but this was rather
> unstable).
>
>
>
> After reading the manual I was really impressed by the possibilities of the
> EBImage package. However, unfortunately, I didn't manage to install the
> package (I am not really a computer specialist, so I had some difficulties
> with following the tutorials). I performed the following steps in
> correspondence to the manuals that are published online:
>
>
>
> 1. First, I installed GTK+ from  "http://gladewin32.sf.net" (since "
> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_2.16.0-20090317_win32.zip"
> and "http://www.gtk.org/download-windows.html" didn't function properly).
> In addition, I added to the "C:\GTK\bin" path to the system environment
> PATH variable.
>

Use the version of GTK  specified in the EBImage installation vignette:
http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/doc/EBImage-installation.pdf

The version specified is gtk+-2.0 2.12.9.


>
>
> 2. Second, I installed ImageMagick from "
> http://www.imagemagick.org/script/binary-releases.php#windows" and placed
> in the following folder "C:\ImageMagick". During the installation of
> ImageMagick I checked the checkbox of 'Install development headers and
> libraries' (the 'Update executable search path' was already checked).
>
>
>
> 3. Third, I downloaded the source zip-package from "
> http://www.bioconductor.org/packages/release/bioc/html/EBImage.html" (I
> tried both 'EBImage_3.10.0.tar.gz' and 'EBImage_3.10.0.zip'). In RGui I
> subsequently used the botton 'Install package(s) from local zip files...'
> (Menu of Packages). Resulting in the following two lines in the console:
>
>> utils:::menuInstallLocal()
>
> package 'EBImage' successfully unpacked and MD5 sums checked
>
> updating HTML package descriptions
>
>
>
> After this the problems appeared: When trying to load the package
> (library("EBImage")):
>
>> library("EBImage")
>
> Error in library.dynam(lib, package, package.lib) :
>
>  shared library 'EBImage' not found
>
> In addition: Warning message:
>
> package 'EBImage' was built under R version 2.14.0
>
> Error: package/namespace load failed for 'EBImage'
>
>


Install EBImage as recommended by its page:
http://bioconductor.org/packages/release/bioc/html/EBImage.html

namely:
source("http://bioconductor.org/biocLite.R")
biocLite("EBImage")

Dan

>
> Perhaps important to know I have Windows XP Professional on my laptop. I
> really hope that you know the solution to this problem. Sorry, for this
> inconvenience. Please, let me know if you require more information. In
> advance, many thanks for your time. I am really appreciative for your help!
>
>
>
> Best regards,
>
>
>
> Jordi
>
>        [[alternative HTML version deleted]]
>
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