[BioC] : [R] Problems wih EBImage for windows 7 --Loading required package: abind Error in library.dynam(lib, package, package.lib) : shared library 'EBImage' not found--SOLVED

Sun Dec 19 01:07:21 CET 2010

I am posting this to help all of the Noob's like me still on Windows Boxes.

1.  I was able to make this work on Win7 without building from source.  I was able to use the latest release of ImageMagic :  ImageMagick-6.6.6-5-Q16-windows-dll.exe
2.  One dependency not listed (that I could see) was on an R package called abind which is a generalization of the rbind and cbind functions
3.  You need to make sure that your R installation is up to date (mine below 2.10 and the latest version of EBImage is for 2.12)
4.  If anyone runs into trouble with this issue, I am happy to relate what I learned.

Thanks,

Evan Misshula
emisshula at jjay.cuny.edu
________________________________________
From: Evan Misshula
Sent: Friday, December 17, 2010 10:28 AM
To: Gregoire Pau
Subject: RE: [BioC] : [R] Problems wih EBImage for windows 7

Hi Gregoire,

Thank you so much.  I tried to follow the direction to the best of my limited ability and I tried to highlight where I was unsure.
Please let me know if additional information would help.

1. gtk2-runtime-2.16.6-2010-05-12-ash.exe  --- from
http://gtk-win.sourceforge.net/home/index.php/Downloads

I think the link you gave me only had the source code and I am not
sure how to compile it.

Here is the path:

PATH=C:\Ruby192\bin;C:\Program Files\ImageMagick-6.6.6-Q16;C:\pik\;C:\Ruby192\bin;C:\Windows\system32;C:\Windows;C:\Windows\system32\wbem;c:\program files\common files\microsoft shared\windows live;C:\Windows\system32\windowspowershell\v1.0;c:\Ruby192\lib\ruby\gems\1.9\bin;c:tools\;c:\program files\intel\wifi\bin;c:\program files\common files\intel\wirelesscommon;c:\program files\common files\lenovo;c:\program files\common files\roxio shared\10.0\dllshared;c:\program files\common files\roxio shared\dllshared;c:\program files\lenovo\access connections;c:\program files\microsoft sql server\90\tools\binn;c:\program files\microsoft sql server\100\tools\binn;c:\program files\microsoft sql server\100\dts\binn;c:\program files\gtksharp\2.12\bin;c:\program files\quicktime\qtsystem;c:\program files\windows live\shared;c:\lf9556\bin;C:\Program Files\MATLAB_SV71\bin\win32;C:\Program Files\MATLAB\R2010b\bin;C:\Program Files\QuickTime\QTSystem\;C:\gtk2\bin

2. ImageMagick-6.6.6-5-Q16-windows-dll.exe ---from
http://www.imagemagick.org/script/binary-releases.php

The instructions say "During installation, the checkboxes `Update exe-
cutable search path' and `Install developement headers and libraries'
must be checked on."

I clicked "Install development headers and libraries for C and C++"
but there was no option that I saw for `Update exe-
cutable search path'.  I did tick 'Add application directory to your
system directory', I am not sure if that is the same thing.

The png file of the option screen is attached.

3.http://www.imagemagick.org/script/binary-releases.php ---from
http://www.bioconductor.org/packages/release/bioc/html/EBImage.html

I used the intall packages from local zip files on the R gui.

> utils:::menuInstallLocal()
package 'EBImage' successfully unpacked and MD5 sums checked
> library("EBImage")
Loading required package: abind
Error in library.dynam(lib, package, package.lib) :
  shared library 'EBImage' not found
In addition: Warning message:
package 'EBImage' was built under R version 2.12.0
Error: package/namespace load failed for 'EBImage'
>

4. SessionInfo()

> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] abind_1.1-0

loaded via a namespace (and not attached):
[1] tools_2.10.1

________________________________________
From: Gregoire Pau [gregoire.pau at embl.de]
Sent: Friday, December 17, 2010 5:41 AM
To: Evan Misshula
Cc: bioconductor at r-project.org
Subject: Re: [BioC] : [R] Problems wih EBImage for windows 7

Hi Evan,

Sure. EBImage works fine on Windows. The issue you're mentioning has
been fixed in the last release of Bioconductor, in October. Please use
the latest release version of EBImage, version 3.6.0, available here:
http://www.bioconductor.org/packages/release/bioc/html/EBImage.html

If it still doesn't work, could please give us the usual stuff: R's
sessionInfo(), EBImage, GTK+ and ImageMagick version numbers.

 > There appear to be no old binaries of 6.5.x to drop back to.
There are many, located at
http://image_magick.veidrodis.com/image_magick/windows/
Try this one, which works fine with my Windows platform:
http://image_magick.veidrodis.com/image_magick/windows/ImageMagick-6.6.1-4.zip

Hope this helps,

Cheers,

Greg
---
Gregoire Pau
EMBL Research Officer
http://www.embl.de/~gpau/

On 16/12/10 23:32, Evan Misshula wrote:
> Hi Gregiore,
> Has any progress been made on this issue?  I am a windows user who also installed GTK+ and the latest version of ImageMagick 6.6.6-5-dll.exe before discovering the binaries do not work for windows 7.  There appear to be no old binaries of 6.5.x to drop back to.  I am too unsophisticated to attempt a build.
> Thank you for your update.
>
> Best,
>
> Evan Misshula
> CUNY John Jay
>
>
> From: Gregoire Pau<gregoire.pau at ...>
> Subject: Re: [R] Poblems wih EBImage
> Newsgroups: gmane.science.biology.informatics.conductor
> Date: 2010-04-17 21:13:19 GMT (34 weeks, 5 days, 1 hour and 13 minutes ago)
>
> Hello Heberto,
>
> The issue you are reporting seems to be due to a recent modification of
> the ImageMagick API, on which EBImage relies on to read/write images. We
> are currently fixing this issue. In the meanwhile, please use a previous
> version of ImageMagick (such as 6.5.x).
>
> Best regards,
>
> Greg
> ---
> Gregoire Pau
> EMBL Research officer
> http://www.ebi.ac.uk/~gpau/
>
> R Heberto Ghezzo, Dr wrote:
>> hello Gregoire
>> Yes, I installed with ' Install develepment headers'
>> If I open a command prompt and typed gtk-demo the corresponding gtk windows appers
>> If I type convert the usage of convert appears from ImageMagick-6.6.1-2
>> So far I think I did everything as requared!
>> Any more suggestions
>> Heberto Ghezzo
>>
>>
>> ________________________________________
>> From: Gregoire Pau [gregoire.pau at ...]
>> Sent: Friday, April 16, 2010 12:37 PM
>> To: R Heberto Ghezzo, Dr
>> Cc: r-help at ...
>> Subject: Re: [R] Poblems wih EBImage
>>
>> Hello,
>>
>> EBImage is a Bioconductor package: please post on the Bioconductor
>> mailing list.
>>
>> EBImage requires the libraries ImageMagick and GTK+ to be installed. Did
>> you follow the instructions of the installation manual ?
>> http://www.bioconductor.org/packages/release/bioc/html/EBImage.html
>>
>> It looks like EBImage cannot locate ImageMagick and GTK+. Are they
>> working properly (try gtk-demo and convert in the command line) ? Did
>> you add the GTK path in the system path (most likely c:\gtk\bin) ? Did
>> you tick the "Install developement headers and libraries" checkbox when
>> installing ImageMagick ?
>>
>> Hope this helps,
>>
>> Regards,
>>
>> Greg
>> ---
>> Gregoire Pau
>> EMBL Research Officer
>> http://www.embl.de/~gpau/
>>
>>
>> R Heberto Ghezzo, Dr wrote:
>>> Hello, Working with Windows 7 in a HP laptop with R-2.10.1
>>> I download and installed ImageMagick-6.3.7.7-Q16-Windows-dll.exe and GTK 2.12.9-win32-2, then
> downloaded and installed from local file EBImage_3.2.0.zip and I got:
>>>> library(EBImage)
>>> Loading required package: abind
>>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>>    unable to load shared library 'C:/Programs/R/Cran/EBImage/libs/EBImage.dll':
>>>    LoadLibrary failure:  The specified module could not be found.
>>>
>>> In addition: Warning message:
>>> package 'abind' was built under R version c(2, 5, 0) and help will not work correctly
>>> Please re-install it
>>> Error: package/namespace load failed for 'EBImage'
>>> the location "C:\Programs\R\Cran\EBImage\libs\EBImage.dll" exists
>>> Can somebody tell me what is wrong?
>>> Thanks
>>> Heberto Ghezzo
>>> McGill University
>>> Canada
>>> ______________________________________________
>>> R-help at ... mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
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