[BioC] EBImage installation problem on Linux

[Wolfgang Huber]

Dear Rama

please use the current release of R and Bioconductor. You are using an 
outdated version (R2.8, Bioc 2.3).

Installation of R is described here:
http://www.bioconductor.org/docs/install/

	Best wishes
	Wolfgang


quantrum75 wrote:
> Hi Group,
> I am trying to install the EBImage package on my linux box. I have the latest version of Ubuntu, GTK2.0 and Image magick. The error which I get is as follows...Could anyone give me an idea what I am doing wrong?
> Thanks in advance.
> Rama
> 
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("EBImage")
> Running biocinstall version 2.3.13 with R version 2.8.1 
> Your version of R requires version 2.3 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
> Â  argument 'lib' is missing: using '/home/rama/R/i486-pc-linux-gnu-library/2.8'
> trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/EBImage_2.6.0.tar.gz'
> Content type 'application/x-gzip' length 1425422 bytes (1.4 Mb)
> opened URL
> ==================================================
> downloaded 1.4 Mb
> 
> * Installing *source* package 'EBImage' ...
> checking for Magick-config... yes
> * found ImageMagick version 6.5.4 Q16 
> * found ImageMagick includes in -I/usr/local/include/ImageMagick
> checking for pkg-config... yes
> * compiling with GTK+ support
> -----------------------------------------------------
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include     -DUSE_GTK -DGLIB_GETTEXT -D_REENTRANT -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/directfb -I/usr/include/libpng12 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -Wall -I/usr/local/include/ImageMagick -fopenmp -I/usr/local/include/ImageMagick  -fpic  -g -O2 -c colors.c -o colors.o
> In file included from colors.c:1:
> colors.h:6:32: error: magick/ImageMagick.h: No such file or directory
> In file included from colors.c:1:
> colors.h:13: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.h:14: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.h:15: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.h:16: error: expected ‘)’ before ‘*’ token
> colors.h:17: error: expected ‘)’ before ‘*’ token
> colors.h:18: error: expected ‘)’ before ‘*’ token
> colors.h:19: error: expected ‘)’ before ‘*’ token
> colors.h:20: error: expected ‘)’ before ‘*’ token
> colors.c:24: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.c:25: error: expected ‘)’ before ‘*’ token
> colors.c:26: error: expected ‘)’ before ‘*’ token
> colors.c:27: error: expected ‘)’ before ‘*’ token
> colors.c: In function ‘lib_channel’:
> colors.c:33: error: ‘Image’ undeclared (first use in this function)
> colors.c:33: error: (Each undeclared identifier is reported only once
> colors.c:33: error: for each function it appears in.)
> colors.c:33: error: ‘image’ undeclared (first use in this function)
> colors.c:35: warning: implicit declaration of function ‘vector2image1D’
> colors.c:40: warning: implicit declaration of function ‘image1D2INTEGER’
> colors.c:40: warning: assignment makes pointer from integer without a cast
> colors.c:43: warning: implicit declaration of function ‘image1D2REAL’
> colors.c:43: warning: assignment makes pointer from integer without a cast
> colors.c:46: warning: assignment makes pointer from integer without a cast
> colors.c:49: warning: assignment makes pointer from integer without a cast
> colors.c:52: warning: assignment makes pointer from integer without a cast
> colors.c:55: warning: assignment makes pointer from integer without a cast
> colors.c:58: warning: assignment makes pointer from integer without a cast
> colors.c:61: warning: assignment makes pointer from integer without a cast
> colors.c:64: warning: implicit declaration of function ‘image1D2CHAR’
> colors.c:64: warning: assignment makes pointer from integer without a cast
> colors.c:67: warning: implicit declaration of function ‘DestroyImage’
> colors.c: At top level:
> colors.c:75: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.c:118: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.c:133: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> colors.c:150: error: expected ‘)’ before ‘*’ token
> colors.c:187: error: expected ‘)’ before ‘*’ token
> colors.c:199: error: expected ‘)’ before ‘*’ token
> colors.c:236: error: expected ‘)’ before ‘*’ token
> colors.c:248: error: expected ‘)’ before ‘*’ token
> make: *** [colors.o] Error 1
> chmod: cannot access `/home/rama/R/i486-pc-linux-gnu-library/2.8/EBImage/libs/*': No such file or directory
> ERROR: compilation failed for package 'EBImage'
> ** Removing '/home/rama/R/i486-pc-linux-gnu-library/2.8/EBImage'
> 
> The downloaded packages are in
> Â Â Â  /tmp/Rtmpp8W5xS/downloaded_packages
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
> Â  installation of package 'EBImage' had non-zero exit status
> 
> 
> 
> 
>       
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