[BioC] (no subject)
Patrick Aboyoun
paboyoun at fhcrc.org
Mon Nov 17 19:49:43 CET 2008
Monnie,
As you mentioned, Rgraphviz requires Graphviz being installed on your
machine. The BioC Mac OS X build machines both use the Graphviz
distribution located at Simon Urbanek's research site:
http://r.research.att.com/
http://r.research.att.com/graphviz-2.12.dmg
Here is a look at the dependencies for Rgraphviz shared object on the Mac:
pitt:~/sandbox/Rgraphviz/libs/i386 biocbuild$ otool -L Rgraphviz.so
Rgraphviz.so:
Rgraphviz.so (compatibility version 0.0.0, current version 0.0.0)
/usr/local/lib/libgvc.3.dylib (compatibility version 4.0.0, current
version 4.0.0)
/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/libR.dylib
(compatibility version 2.8.0, current version 2.8.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
(compatibility version 150.0.0, current version 368.35.0)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 88.3.10)
If you don't use the Graphviz mentioned above, make sure you either
change the link to libgvc.3.dylib or install Graphviz in /usr/local.
Patrick
McGee, Monnie wrote:
> Dear Martin,
>
> Thanks for your help. It seems to me that both Rgraphviz and Graphviz must be compiled from source code, at least, that's what the README file leads me to believe. I don't suppose that anyone out there knows how to get Rgraphviz working using binaries?
>
> Anyway, I search my computer for libgvc.3.dylib and the file does not exist. Perhaps this goes back to the source code issue. Also, here are the results when I type Sys.getenv("LD_LIBRARY_PATH") on my computer:
>
>
>> Sys.getenv("LD_LIBRARY_PATH")
>>
> LD_LIBRARY_PATH
> ""
> I suppose that LD_LIBRARY_PATH should say something different, but I am not sure what it should be or how to set it.
>
> I am going to try compiling from source and see what happens.
>
> Thanks again,
> Monnie
> ________________________________________
> From: Martin Morgan [mtmorgan at fhcrc.org]
> Sent: Monday, November 17, 2008 5:28 PM
> To: McGee, Monnie
> Cc: Raffaele calogero; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] (no subject)
>
> Hi Monnie -- I'm hoping that someone with Mac experience will provide
> specific guidance. The error message says that the file libgvc.3.dylib
> is not found. This is likely because it is installed somewhere that
> Rgraphviz does not know about. I don't know if this is an issue with
> the way graphviz was installed on your Mac (where is libgvc.3.dylib?)
> or how Rgraphviz looks for this package (what does
> Sys.getenv("LD_LIBRARY_PATH") say from within R?).
>
> The 'README' file I was referring to was the README file in the
> Rgraphviz package; visit
>
> http://bioconductor.org/packages/2.3/bioc/html/Rgraphviz.html
>
> download and unpack the 'Package source' link to view.
>
> Martin
>
> "McGee, Monnie" <mmcgee at mail.smu.edu> writes:
>
>
>> Dear Martin,
>>
>> Thank you. What are the steps for Macintosh? I've copied in the error and my sessionInfo below.
>>
>> As far as I can tell, the version of Graphviz that I downloaded for the Mac (Version 2.20 (2.20.3)) does not have a README file. Do I need to download that from the Graphviz website, also?
>>
>> Thanks,
>> Monnie
>>
>> ##### Error I received ######
>>
>>> library(Rgraphviz)
>>>
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared library '/Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
>> dlopen(/Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.3.dylib
>> Referenced from: /Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so
>> Reason: image not found
>> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>> Error: package/namespace load failed for 'Rgraphviz'
>>
>> ### Session Info #####
>>
>>> sessionInfo()
>>>
>> R version 2.7.2 (2008-08-25)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] tools grid stats graphics grDevices utils datasets methods
>> [9] base
>>
>> other attached packages:
>> [1] Rintact_1.2.0 hypergraph_1.12.0 XML_1.96-0 yeastExpData_0.9.11
>> [5] RBGL_1.16.0 RColorBrewer_1.0-2 Biobase_2.0.1 graph_1.18.1
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.11
>>
>> ________________________________________
>> From: Martin Morgan [mtmorgan at fhcrc.org]
>> Sent: Monday, November 17, 2008 5:10 PM
>> To: Raffaele calogero
>> Cc: McGee, Monnie; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] (no subject)
>>
>> Raffaele calogero wrote:
>>
>>> On Mon, Nov 17, 2008 at 4:59 PM, McGee, Monnie <mmcgee at mail.smu.edu> wrote:
>>> Dear Monnie,
>>> thank you for your answer.
>>> I Rgraphviz is always somehow problematic on windows computers.
>>> I do not think I have to download Graphviz since it was never
>>> necessary before on packages compiled for windows. The strange point
>>> is that I can load and use without problems the Bioconductor 2.1
>>> Rgraphviz version.
>>>
>> Windows versions of Rgraphviz working with R 2.7.* or 2.8.* require that
>> you have graphviz installed. It must be a specific version of Graphviz.
>> The README file for the CURRENT version (for use with R-2.8.*) of
>> Rgraphviz says
>>
>>
>>> Windows
>>> =======
>>>
>>> Nov 4, 2008
>>>
>>> Here are the steps to build Rgraphviz on Windows:
>>>
>>> o. install graphviz ***2.20.3*** Windows ***binary*** distribution from
>>> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.msi
>>> , say, in dir $DIR. We use the following as an example:
>>> C:\Graphviz-2.21
>>> . If you install it in other dir, just use your dir correspondingly.
>>>
>>> o. set the following Windows environment variables accordingly
>>> (control panel -> systems -> Advanced -> Environment Variables ):
>>> (a) create new user variables:
>>> GRAPHVIZ_INSTALL_DIR (e.g., C:\Graphviz-2.21)
>>> GRAPHVIZ_INSTALL_MAJOR (e.g., 2)
>>> GRAPHVIZ_INSTALL_MINOR (e.g., 20)
>>>
>>> Notice the way "\/" are used for the paths above.
>>>
>>> (b) add to user variable 'path': $GRAPHVIZ_INSTALL_DIR/bin
>>> e.g., C:\Graphviz-2.21\bin
>>>
>>> o. run "R CMD INSTALL ...Rgraphviz" as usual
>>>
>> The specific version of graphviz is different for R-2.7.*.
>>
>> Martin
>>
>>
>>> Cheers
>>> Raffaele
>>>
>>>
>>>> Dear Raffaele,
>>>>
>>>> I have had the same problem on my Macintosh computer. I sent an e-mail to the list last Thursday, but I have not yet received a reply.
>>>>
>>>> One question for you - have you downloaded Graphviz? Rgraphviz will not work without Graphviz. The website is www.graphiviz.org.
>>>>
>>>> I downloaded Graphiviz, and it didn't solve my problem, but it may solve yours.
>>>>
>>>> Good Luck!
>>>> Monnie
>>>>
>>>>
>>>> Message: 1
>>>> Date: Sun, 16 Nov 2008 16:39:14 +0100
>>>> From: rcaloger <raffaele.calogero at gmail.com>
>>>> Subject: [BioC] Rgraphviz error under Windows
>>>> To: bioconductor at stat.math.ethz.ch
>>>> Message-ID: <49203EA2.7030403 at unito.it>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>
>>>> HI,
>>>> I installed Rgraphviz_1.20.2.zip without error on Windows Vista 32 bits
>>>> Centrino duo with 2Gb RAM.
>>>> But when I tryed to load the library:
>>>> library(Rgraphviz)
>>>> I got the following error:
>>>> Error in get(hookname, envir = env, inherits = FALSE) :
>>>> cannot allocate memory block of size 2.2 Gb
>>>> Error: package/namespace load failed for 'Rgraphviz'
>>>>
>>>> This happens on an clean R session without anything loaded.
>>>> When I tryed to install the Rgraphviz from Bioconductor 2.2
>>>> Rgraphviz_1.18.1.zip, instllation succeded but the loading of the
>>>> library produced an other error:
>>>> > library(Rgraphviz)
>>>> Loading required package: graph
>>>> Loading required package: grid
>>>> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>>>> unable to load shared library
>>>> 'C:/R/R-2.8.0/library/Rgraphviz/libs/Rgraphviz.dll':
>>>> LoadLibrary failure: Unable to find the specified module.
>>>>
>>>> Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>>>> Error: package/namespace load failed for 'Rgraphviz'
>>>>
>>>> Loading of the Rgraphviz lib was instead successful using
>>>> Rgraphviz_1.16.0.zip from Bioconductor 2.1
>>>>
>>>> Any suggestion how to solve Rgraphviz loading problem?
>>>> Raffaele
>>>>
>>>
>>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
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