[BioC] EBImage installation problem on Linux
Gregoire Pau
gregoire.pau at embl.de
Sun Jul 19 17:45:57 CEST 2009
Dear Rama,
It looks like your ImageMagick (IM) installation is messed up.
First, please make sure that both the Ubuntu IM main package
(ImageMagick) and the Ubuntu IM development package (sometimes referred
as ImageMagick-devel) are installed, as mentioned in the 'How to install
EBImage' file.
EBImage uses the command 'Magick-config --cppflags' to localize IM
components and according to your output, it seems that the IM headers
are in '/usr/local/include/ImageMagick'
But your 'ls' command shows that the IM headers are in
'/usr/include/ImageMagick/magick', contradicting the results given before.
It seems that you have two IM installations in parallel on your system:
an Ubuntu packaged one (without the development component) and a
non-packaged, manually installed version. Or maybe did you rename some
directories by mistake ?
I would suggest you to (re)install both the Ubuntu ImageMagick main and
development packages. If you have installed ImageMagick manually, then
you could uninstall the Ubuntu ImageMagick package to avoid a version
clash. After these steps, please check that the header files are
present in the directory returned by the command 'Magick-config --cppflags'.
Best,
Greg
---
Gregoire Pau
EMBL Research officer
http://www.ebi.ac.uk/~gpau/
quantrum75 wrote:
> Dear Wolfgang,
> Thank you for your reply. As per your advice, I reinstalled the software and tried to install EBImage with biocLite. However, I still get the same error. I also tried to locate the file in the location and directory (see details below) and the file was indeed there. So I am not sure EBImage is giving the error that Imagemagick.h is not there.
> I shall look forward to any guidance on the subject.
> Thanks
> Rama
>
> INSTALLATION -
> Running biocinstall version 2.4.11 with R version 2.9.1
> Your version of R requires version 2.4 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/2.9'
> trying URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/EBImage_3.0.3.tar.gz'
> Content type 'application/x-gzip' length 10222583 bytes (9.7 Mb)
> opened URL
> ==================================================
> downloaded 9.7 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 EBImage.c -o EBImage.o
> In file included from EBImage.c:8:
> conversions.h:6:32: error: magick/ImageMagick.h: No such file or directory
> In file included from EBImage.c:8:
> conversions.h:12: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
> conversions.h:13: error: expected ‘)’ before ‘*’ token
> EBImage.c:40:30: error: wand/magick-wand.h: No such file or directory
> EBImage.c: In function ‘R_init_EBImage’:
> EBImage.c:158: warning: implicit declaration of function ‘MagickWandGenesis’
> EBImage.c: In function ‘R_unload_EBImage’:
> EBImage.c:166: warning: implicit declaration of function ‘MagickWandTerminus’
> make: *** [EBImage.o] Error 1
> ERROR: compilation failed for package ‘EBImage’
> * Removing ‘/home/rama/R/i486-pc-linux-gnu-library/2.9/EBImage’
>
> The downloaded packages are in
>    ‘/tmp/RtmpdB9twt/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, :
> Â installation of package 'EBImage' had non-zero exit status
>
> LOCATION OF IMAGEMAGICK.H
>
> rama at Durga:/usr/include/ImageMagick/magick$ ls
> animate.h    coder.h      delegate.h  gem.h         log.h           mime.h       profile.h   segment.h    timer.h
> annotate.h   color.h      deprecate.h geometry.h    magic.h         module.h     property.h  semaphore.h  token.h
> api.h        colorspace.h display.h   hashmap.h     magick-config.h monitor.h    quantize.h  shear.h      transform.h
> artifact.h   compare.h    distort.h   identify.h    MagickCore.h    montage.h    quantum.h   signature.h  type.h
> blob.h       composite.h  draw.h      image.h       magick.h        option.h     random_.h   splay-tree.h utility.h
> cache.h      compress.h   effect.h    ImageMagick.h magick-type.h   paint.h      registry.h  statistic.h  version.h
> cache-view.h configure.h  enhance.h   layer.h       matrix.h        pixel.h      resample.h  stream.h     widget.h
> cipher.h     constitute.h exception.h list.h        memory_.h       prepress.h   resize.h    string_.h    xml-tree.h
> client.h     decorate.h   fx.h        locale_.h     methods.h       PreRvIcccm.h resource_.h threshold.h  xwindow.h
>
>
>
> --- On Sat, 7/18/09, Wolfgang Huber <huber at ebi.ac.uk> wrote:
>
> From: Wolfgang Huber <huber at ebi.ac.uk>
> Subject: Re: [BioC] EBImage installation problem on Linux
>
> Cc: bioconductor at stat.math.ethz.ch
> Date: Saturday, July 18, 2009, 4:18 PM
>
> 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/
>
> Â Â Â Best wishes
> Â Â Â 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, :
>>  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
>>    /tmp/Rtmpp8W5xS/downloaded_packages
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, :
>>  installation of package 'EBImage' had non-zero exit status
>>
>>
>>
>>
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>>
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