[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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