[BioC] FW: Graphviz in Vista64
Kasper Daniel Hansen
khansen at stat.berkeley.edu
Mon Mar 2 21:43:55 CET 2009
Fraser
This is not really related to Vista 64 bit anymore. It is instead
related to getting Rgraphviz to work with the new version of Graphviz,
on all platforms.
In principle it is not too hard to do. I'll have a look tonight, it is
probably easier to just do it, than to explain in detail what needs to
be done. It took me a while to understand last time I went through it.
But do expect to receive some tarballs over the next couple of days,
testing out the "solution".
Further communication is probably more fruitful off-list.
Kasper
On Mar 2, 2009, at 12:01 , Sim, Fraser wrote:
> Hi Kasper,
>
> How would I go about doing this? I'm willing to learn what's necessary
> but would appreciate any help. I began using graphViz to visualize
> gene
> networks and have written code for this using graphViz. Currently I
> have
> to render these using a separate WinXP box. I think it will be a
> worthwhile effort as more and more people will use Vista (and then
> Windows 7 when it comes out) and Bioconductor will need to support it
> sooner or later.
>
> Cheers,
> Fraser
>
> -----Original Message-----
> From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu]
> Sent: Monday, March 02, 2009 2:42 PM
> To: Sim, Fraser
> Cc: Martin Morgan; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] FW: Graphviz in Vista64
>
> This looks as what I predicted in my email: the developers of Graphviz
> has yet again changed the internal structures.
>
> Rgraphviz needs to be updated to fix this and the autoconf script
> needs to be modified yet again. Unless someone is dying to do this
> right now, this might take a while.
>
> Kasper
>
>
> On Mar 2, 2009, at 11:15 , Sim, Fraser wrote:
>
>> Hi Martin,
>>
>> Luckily enough I had already tried building 32-bit R from source,
>> so I
>> tried to install the Rgraphviz package from source.
>>
>> Here is the result (also see comments at end):
>>
>> installing to 'C:\Users\FSIM/R/win-library/2.8'
>>
>> ---------- Making package Rgraphviz ------------
>> GRAPHVIZ_INSTALL_DIR=C:\/Progra~2\/Graphviz2.21
>> GRAPHVIZ_INSTALL_MAJOR=2
>> GRAPHVIZ_INSTALL_MINOR=21
>> adding build stamp to DESCRIPTION
>> installing NAMESPACE file and metadata
>> making DLL ...
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> LL_funcs.c -
>> o LL_funcs.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> Rgraphviz.c
>> -o Rgraphviz.o
>> Rgraphviz.c:18: warning: C99 inline functions are not supported;
>> using
>> GNU89
>> Rgraphviz.c:18: warning: to disable this warning use -fgnu89-inline
>> or
>> the gnu_i
>> nline function attribute
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> RgraphvizIni
>> t.c -o RgraphvizInit.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> agopen.c -o
>> agopen.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> agread.c -o
>> agread.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> agwrite.c -o
>> agwrite.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> bezier.c -o
>> bezier.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> buildEdgeLis
>> t.c -o buildEdgeList.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> buildNodeLis
>> t.c -o buildNodeList.o
>> gcc -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
>> -DGRAPHVIZ_MAJOR=2 -
>> DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include -O3 -Wall -c
>> doLayout.c -
>> o doLayout.o
>> doLayout.c: In function 'getEdgeLocs':
>> doLayout.c:127: error: 'textlabel_t' has no member named 'p'
>> doLayout.c:128: error: 'textlabel_t' has no member named 'p'
>> doLayout.c: In function 'getNodeLayouts':
>> doLayout.c:234: error: 'textlabel_t' has no member named 'p'
>> doLayout.c:235: error: 'textlabel_t' has no member named 'p'
>> make[3]: *** [doLayout.o] Error 1
>> make[2]: *** [srcDynlib] Error 2
>> make[1]: *** [all] Error 2
>> make: *** [pkg-Rgraphviz] Error 2
>> *** Installation of Rgraphviz failed ***
>>
>> Removing 'C:/Users/FSIM/R/win-library/2.8/Rgraphviz'
>> Restoring previous 'C:/Users/FSIM/R/win-library/2.8/Rgraphviz'
>>
>>
>> *****************************************************************
>>
>> Interestingly enough when I ran RGUI.exe to generate the crash with
>> the
>> Insight debugger through Cygwin, I found out that the code that
>> failed
>> occurred in getNodeLayouts (possibly on line 761).
>>
>> This looks like it corresponds to the error on compile that occurred
>> in
>> function 'getNodeLayouts'?
>>
>> What next?
>>
>> Thanks,
>> Fraser
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
>> Sent: Monday, March 02, 2009 1:09 PM
>> To: Sim, Fraser
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] FW: Graphviz in Vista64
>>
>> Hi Fraser -- I think your best bet is to build Rgraphviz from source,
>> rather than using the Windows binary from Bioconductor. This will
>> allow you to link with the specific version of graphviz that you
>> 'know' works on Vista64, otherwise you're relying too strongly on
>> compile-time assumptions (about the linked graphviz DLLs) that you
>> know to be incorrect.
>>
>> Since R does not yet build on 64bit windows, I guess the path forward
>> is to build Rgraphviz with the appropriate graphviz from source on a
>> 32bit windows, and to use that with 32bit graphviz on Vista. It would
>> not be too surprising if this contiues to be problematic -- memory
>> allocation bugs (in both Rgraphviz and graphviz) that are hidden
>> under
>> 32bit windows might well be exposed under 64bit Vista.
>>
>> Building Windows packages from source requires extra tooling, but is
>> not too complicated. See
>>
>> http://www.murdoch-sutherland.com/Rtools/
>>
>> no need for the 'optional' components listed on that page. There are
>> additional instructions for building Rgraphviz in the README file of
>> that package.
>>
>> Martin
>>
>> "Sim, Fraser" <Fraser_Sim at urmc.rochester.edu> writes:
>>
>>> Hi Kasper,
>>>
>>> The graphviz installations that I have tried include the following
>>> versions downloaded from http://www.graphviz.org/ :
>>>
>>> 2.20.3 - In R, loads Rgraphviz package fine but crashes when layout
>>> performed. Also, GVedit.exe did not work correctly and the graphViz
>>> developer, Arif, suggested I try the developer version.
>>>
>>> Tried both:
>>> graphviz-2.21.20090202.1215.msi
>>> graphviz-mingw-2.21.20090202.1215.msi
>>>
>>> Both versions worked via GVedit.exe. The package loads but now
>>> with a
>>> warning. RGUI.EXE continues to crash on attempts to perform
>>> layoutGraph().
>>
>>
>>
>>> The term 'crash' here means, a pop-up dialog from Vista informing me
>>> that RGUI.EXE has stopped working and Windows will close the
>>> program.
>>> There are no additional details.
>>>
>>> I have installed and used Rgraphviz on a number of XP32 boxes and so
>> am
>>> familiar with the quirks required to get it working. This is an
>> entirely
>>> different problem.
>>>
>>> I have switched to Vista64 to work with larger datasets requiring
>>> additional memory.
>>>
>>> Thanks,
>>> Fraser
>>>
>>> -----Original Message-----
>>> From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu]
>>> Sent: Monday, March 02, 2009 11:48 AM
>>> To: Sim, Fraser
>>> Cc: Bioconductor at stat.math.ethz.ch
>>> Subject: Re: [BioC] Graphviz in Vista64
>>>
>>> Most likely something is wrong with your graphviz installation, but
>>> since you don't provide any details about that, it is impossible to
>>> help. We would also like to see the actual crash output from R or a
>>> better description of what you mean by "crash"
>>>
>>> Kasper
>>>
>>> On Mar 2, 2009, at 7:48 , Sim, Fraser wrote:
>>>
>>>> Hi Bioconductors,
>>>>
>>>> Has anyone successfully used the Rgraphviz package to plot graphs
>>>> in
>> R
>>>> under Vista64??
>>>>
>>>> I have found that RGUI.EXE crashes upon execution of the
>>>> layoutGraph
>>>> step.
>>>>
>>>> Running the following reliably crashes R.
>>>>
>>>> library("Rgraphviz")
>>>> g = new("graphNEL", nodes = c("a","b","c"))
>>>> debug(Rgraphviz:::graphLayout)
>>>> sessionInfo()
>>>> layoutGraph(g)
>>>>
>>>> Thanks,
>>>> Fraser
>>>>
>>>> PS. The crash occurs in :
>>>>
>>>> Rgraphviz:::graphLayout
>>>>
>> .Call
>> ("Rgraphviz_doLayout",graph,as.integer(type),PACKAGE="Rgraphviz")
>>>>
>>>> PPS.
>>>> sessionInfo()
>>>>
>>>> R version 2.8.1 (2008-12-22)
>>>> i386-pc-mingw32
>>>>
>>>> locale:
>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>>> States.1252;LC_MONETARY=English_United
>>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>>
>>>> attached base packages:
>>>> [1] grid stats graphics grDevices utils datasets
>>>> methods
>>>>
>>>> [8] base
>>>>
>>>> other attached packages:
>>>> [1] Rgraphviz_1.20.3 graph_1.20.0 rcom_2.0-4
>> rscproxy_1.0-12
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] cluster_1.11.12 tools_2.8.1
>>>>
>>>> _______________________________________________
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>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>> _______________________________________________
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>>
>> --
>> 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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