[BioC] EBImage installation problem on Linux

[Wolfgang Huber]

Dear Jayangshu

what happens when you type "Magick-config" in the command line? It 
appears that it is not installed, or if it is installed, that PATH 
and/or other environment variables are not set. If this sounds confusing 
to you, then perhaps you would best consult a Linux administrator.
Please do follow the installation instructions in the PDF file that 
comes with the EBImage package. They are there for a reason.

Btw, it is not advisable to run R CMD INSTALL as 'root' user. Better to 
create a user-id with restricted rights that can install R and R packages.

	Best wishes
	Wolfgang


On 7/11/12 11:21 AM, Jayangshu Saha [guest] wrote:
>
> Hi Group,
>
> I am trying to install the EBImage package on my linux box. I have the latest version of Red Hat Linux, GTK 2.10.4 and Image magick. The error which I get is as follows...Could anyone give me an idea what I am doing wrong?
> Please find the error message and session info below.
>
> I have already read an earlier post regarding the same issue (https://stat.ethz.ch/pipermail/bioconductor/2009-July/028666.html) and seen the response but I using latest version anyway.
>
>
> Thanks in advance.
>
> Jayangshu
>
>   -- output of sessionInfo():
>
> [root at CS-ORIS-SVR09 local]# R CMD INSTALL EBImage_3.12.0.tar.gz
> * installing to library â/usr/local/lib64/R/libraryâ
> * installing *source* package âEBImageâ ...
> checking for Magick-config... no
> configure: error: "ImageMagick or ImageMagick includes not found!"
> ERROR: configuration failed for package âEBImageâ
> * removing â/usr/local/lib64/R/library/EBImageâ
>
> [root at CS-ORIS-SVR09 local]# R
>
> R version 2.15.0 (2012-03-30)
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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.
>
>> source("http://bioconductor.org/biocLite.R")
> BiocInstaller version 1.4.7, ?biocLite for help
>>      biocLite("EBImage")
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.7.
> Installing package(s) 'EBImage'
> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/EBImage_3.12.0.tar.gz'
> Content type 'application/x-gzip' length 4738660 bytes (4.5 Mb)
> opened URL
> ==================================================
> downloaded 4.5 Mb
>
> * installing *source* package âEBImageâ ...
> checking for Magick-config... no
> configure: error: "ImageMagick or ImageMagick includes not found!"
> ERROR: configuration failed for package âEBImageâ
> * removing â/usr/local/lib64/R/library/EBImageâ
>
> The downloaded source packages are in
>          â/tmp/Rtmpp42hTM/downloaded_packagesâ
> Updating HTML index of packages in '.Library'
> Making packages.html  ... done
> Old packages: 'caTools', 'gplots', 'gregmisc', 'RCurl'
> Update all/some/none? [a/s/n]:
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.7
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber