[BioC] FW: Graphviz in Vista64

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Mon Mar 2 20:15:55 CET 2009

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 ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
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_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
-o Rgraphviz.o
Rgraphviz.c:18: warning: C99 inline functions are not supported; using
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_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
t.c -o RgraphvizInit.o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
agopen.c -o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
agread.c -o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
agwrite.c -o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
bezier.c -o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
t.c -o buildEdgeList.o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
DGRAPHVIZ_MINOR=21 -DWin32 -IC:/R/R-2.8.1/include     -O3 -Wall  -c
t.c -o buildNodeList.o
gcc  -std=gnu99 -IC:/Progra~2/Graphviz2.21/include/graphviz
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?


-----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


no need for the 'optional' components listed on that page. There are
additional instructions for building Rgraphviz in the README file of
that package.


"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
> familiar with the quirks required to get it working. This is an
> 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
>> 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
>> 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
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.12 tools_2.8.1
>> _______________________________________________
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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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