[R-SIG-Mac] Rgraphviz installation problem

William Revelle lists at revelle.net
Mon Aug 21 21:57:16 CEST 2006


Dear R - mac users

I also have been trying to use Rgraphviz with the same problem.

all "dot" plots seem to work, but any attempt to do a "neato" or 
other type makes R crash:

I am running R Version 2.3.1 (2006-06-01)
on a Power Book  Power PC G4 running  10.4.7

I have been able to run Graphviz version 1.13 as a standalone program 
with dot commands generated by R (following a script based upon John 
Fox's sem graph script) or  can use Rgraphviz to do somewhat simpler 
graphs within R.

Using the example code from ?dot
library(Rgraphviz)
Loading required package: graph
Loading required package: Ruuid
>  ?dot
>  set.seed(123)
>  V <- letters[1:10]
>  M <- 1:4
>  g1 <- randomGraph(V, M, .2)
>  plot(g1)
>  plot(g1,"neato")

  *** caught bus error ***
address 0x0, cause 'invalid alignment'

Traceback:
  1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE = "Rgraphviz")
  2: layoutGraph(g)
  3: agopen(x, name = name, layout = TRUE, layoutType = y, attrs = 
attrs,     nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, subGList = 
subGList,     recipEdges = recipEdges)
  4: .local(x, y, ...)
  5: plot(g1, "neato")
  6: plot(g1, "neato")


Here is the Mac problem report:

Date/Time:      2006-08-21 14:53:52.784 -0500
OS Version:     10.4.7 (Build 8J135)
Report Version: 4

Command: R
Path:    /Applications/R.app/Contents/MacOS/R
Parent:  WindowServer [65]

Version: 1.16 (3198)

PID:    26700
Thread: 0

Exception:  EXC_BAD_ACCESS (0x0001)
Codes:      KERN_PROTECTION_FAILURE (0x0002) at 0x00000000

Thread 0 Crashed:
0   libpack.2.dylib               	0x055a20d4 packGraphs + 240 
(pack.c:778)
1   ...plugin_neato_layout.2.dylib	0x07816ff8 neato_layout + 688 
(neatoinit.c:1218)
2   libgvc.2.dylib                	0x0690f510 gvLayoutJobs + 100 
(gvlayout.c:69)
3   libgvc.2.dylib                	0x06912604 gvLayout + 64 (gvc.c:71)
4   Rgraphviz.so                  	0x04aa2754 Rgraphviz_doLayout 
+ 508 (Rgraphviz.c:429)
5   libR.dylib                    	0x01071714 do_dotcall + 764 
(dotcode.c:861)
6   libR.dylib                    	0x0109d818 Rf_eval + 1576 (eval.c:415)
7   libR.dylib                    	0x0109f7c8 do_set + 728 (eval.c:1326)
8   libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
9   libR.dylib                    	0x0109f888 do_begin + 84 (eval.c:1075)
10  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
11  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
12  libR.dylib                    	0x0109f888 do_begin + 84 (eval.c:1075)
13  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
14  libR.dylib                    	0x010a0c80 Rf_applyClosure + 
684 (eval.c:588)
15  libR.dylib                    	0x0109d550 Rf_eval + 864 (eval.c:429)
16  libR.dylib                    	0x0109e5f8 
Rf_evalListKeepMissing + 132 (eval.c:1454)
17  libR.dylib                    	0x0109e768 do_return + 48 (eval.c:1091)
18  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
19  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
20  libR.dylib                    	0x0109f888 do_begin + 84 (eval.c:1075)
21  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
22  libR.dylib                    	0x010a0c80 Rf_applyClosure + 
684 (eval.c:588)
23  libR.dylib                    	0x0109d550 Rf_eval + 864 (eval.c:429)
24  libR.dylib                    	0x0109f7c8 do_set + 728 (eval.c:1326)
25  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
26  libR.dylib                    	0x0109f888 do_begin + 84 (eval.c:1075)
27  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
28  libR.dylib                    	0x010a0c80 Rf_applyClosure + 
684 (eval.c:588)
29  libR.dylib                    	0x0109d550 Rf_eval + 864 (eval.c:429)
30  libR.dylib                    	0x0109f888 do_begin + 84 (eval.c:1075)
31  libR.dylib                    	0x0109d6e4 Rf_eval + 1268 (eval.c:398)
32  libR.dylib                    	0x010a0584 R_execClosure + 
276 (eval.c:673)
33  libR.dylib                    	0x010a0910 R_execMethod + 580 
(eval.c:775)
34  methods.so                    	0x04a7623c R_standardGeneric 
+ 1216 (methods_list_dispatch.c:624)
35  libR.dylib                    	0x010d0f64 do_standardGeneric 
+ 176 (objects.c:1012)
36  libR.dylib                    	0x0109d93c Rf_eval + 1868 (eval.c:418)
37  libR.dylib                    	0x010a0c80 Rf_applyClosure + 
684 (eval.c:588)
38  libR.dylib                    	0x0109d550 Rf_eval + 864 (eval.c:429)
39  org.R-project.R               	0x00032390 
run_REngineRmainloop + 640 (Rinit.c:391)
40  org.R-project.R               	0x0002aa1c -[REngine runREPL] 
+ 68 (REngine.m:167)
41  org.R-project.R               	0x0001d340 main + 680 (main.m:101)
42  org.R-project.R               	0x00002e8c _start + 340 (crt.c:272)
43  org.R-project.R               	0x00002d34 start + 60

Thread 1:
0   libSystem.B.dylib             	0x9001f7ac select + 12
1   org.R-project.R               	0x0000a588 -[RController 
readThread:] + 588 (RController.m:553)
2   com.apple.Foundation          	0x92944194 forkThreadForFunction + 108
3   libSystem.B.dylib             	0x9002bc28 _pthread_body + 96

Thread 2:
0   libSystem.B.dylib             	0x9004a568 syscall_thread_switch + 8
1   com.apple.Foundation          	0x9295c5d0 +[NSThread 
sleepUntilDate:] + 152
2   com.apple.AppKit              	0x937b0a10 -[NSUIHeartBeat 
_heartBeatThread:] + 1100
3   com.apple.Foundation          	0x92944194 forkThreadForFunction + 108
4   libSystem.B.dylib             	0x9002bc28 _pthread_body + 96

Thread 3:
0   libSystem.B.dylib             	0x9000b268 mach_msg_trap + 8
1   libSystem.B.dylib             	0x9000b1bc mach_msg + 60
2   com.apple.CoreFoundation      	0x907dbb78 __CFRunLoopRun + 832
3   com.apple.CoreFoundation      	0x907db47c CFRunLoopRunSpecific + 268
4   com.apple.Foundation          	0x9296b69c 
+[NSURLConnection(NSURLConnectionInternal) _resourceLoadLoop:] + 264
5   com.apple.Foundation          	0x92944194 forkThreadForFunction + 108
6   libSystem.B.dylib             	0x9002bc28 _pthread_body + 96

Thread 4:
0   libSystem.B.dylib             	0x9000b268 mach_msg_trap + 8
1   libSystem.B.dylib             	0x9000b1bc mach_msg + 60
2   com.apple.CoreFoundation      	0x907dbb78 __CFRunLoopRun + 832
3   com.apple.CoreFoundation      	0x907db47c CFRunLoopRunSpecific + 268
4   com.apple.Foundation          	0x9296c7dc +[NSURLCache 
_diskCacheSyncLoop:] + 152
5   com.apple.Foundation          	0x92944194 forkThreadForFunction + 108
6   libSystem.B.dylib             	0x9002bc28 _pthread_body + 96

Thread 5:
0   libSystem.B.dylib             	0x9000b268 mach_msg_trap + 8
1   libSystem.B.dylib             	0x9000b1bc mach_msg + 60
2   com.apple.CoreFoundation      	0x907dbb78 __CFRunLoopRun + 832
3   com.apple.CoreFoundation      	0x907db47c CFRunLoopRunSpecific + 268
4   com.apple.Foundation          	0x92953164 -[NSRunLoop 
runMode:beforeDate:] + 172
5   com.apple.Foundation          	0x9295309c -[NSRunLoop run] + 76
6   com.apple.WebKit              	0x95a68f70 +[WebFileDatabase 
_syncLoop:] + 176
7   com.apple.Foundation          	0x92944194 forkThreadForFunction + 108
8   libSystem.B.dylib             	0x9002bc28 _pthread_body + 96

Good luck.

Bill



At 8:42 AM -0700 8/21/06, Seth Falcon wrote:
>Rob J Goedman <goedman at mac.com> writes:
>
>>  Below (graphviz1.out) the dylibs that get loaded.  And the file I
>>  sourced in. The plot(g1, "dot")
>>  produced the usual plot (until now I have always been using version
>>  Graphviz-2.3), the
>>  plot(g1, "neato") causes the bus error/invalid address.
>
>graphviz 2.3 is rather old.  Can you try upgrading to the latest
>release and see if the problem persists?
>
>_______________________________________________
>R-SIG-Mac mailing list
>R-SIG-Mac at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/r-sig-mac


-- 
William Revelle		http://pmc.psych.northwestern.edu/revelle.html   
Professor			http://personality-project.org/personality.html
Department of Psychology       http://www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/



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