lme4a crash
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On 06/29/2011 03:24 AM, Christopher Philipson wrote:
Hi Ben and mixed modellers,
My apologies. The link you provided is useful, I am working on a simpler example that produces the problem.
The nlmer() model is:
power.law_light2 <- deriv(expression((( ( M0 )^(1-beta)) + (exp(Amax_Int + Amax_Slope * x2))*(1-beta)*x1)^(1/(1-beta))),
c("M0", "Amax_Int","Amax_Slope", "beta"), function(x1, x2, M0, Amax_Int, Amax_Slope, beta) {})
nlmer1<- nlmer(total.mass ~ power.law_light2(day, Treatment, M0, Amax_Int, Amax_Slope, beta) ~
0 + M0 + Amax_Int + Amax_Slope + beta
+ (0 + M0 |Seedling_no2)
+ (0 + Amax_Int|Seedling_no2)
+ (0 + beta |Seedling_no2),
datNEW,
start=mystart,
verbose=TRUE);
In the mean time I have established that R64, does not crash but produces the following error message:
Error in bobyqa(ans at re@theta, obj, ans at re@lower, control = control) :
non-finite objective values not allowed
In addition: Warning message:
In log(.expr8) : NaNs produced
I will try to produce an example that does repeats this
Thanks. The core dump is not so useful (although perhaps one of the other lme4 authors will find it so), but bandwidth is cheap. Just for general information: we have had trouble, for some time now, managing to set up the lme4a code (which has lots of shiny Rcpp stuff under the surface) so that errors emanating from inside C++ code are caught correctly and passed back to the R "surface" rather than crashing R. As in your case, the results seem to be platform-dependent. We have some examples to work on (and just lack time, and in my case knowledge, to spend tracking down and fixing the problems), but another example would still be welcome. Of course, even if the program "only" stops with an error rather than crashing you will still have a problem (albeit a less annoying one), in that the optimization heads to a point that produces NaNs. In the spirit of working around that problem, here are a couple of thoughts: * can you specify "better" starting values, e.g. by starting with the fixed-effect analogue of the model above? (Perhaps you are already doing this.) * your model is very complicated. I hope you have a big data set ... does it work if you eliminate one or more of the random effects? Can you use that approach to sneak up on better starting values? * there doesn't seem to be anything in your model that wouldn't work with nlme (i.e. no crossed random effects -- although if your data set is big nlmer will probably be faster than nlme). Have you tried it in nlme, perhaps with a subset of the data to start?
The sessionInfo() is: [note I have the same situation with r2.13]
R version 2.14.0 Under development (unstable) (2011-06-26 r56223)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lme4a_0.999375-67 MatrixModels_0.2-1 minqa_1.1.15 Rcpp_0.9.4 Matrix_0.999375-50 lattice_0.19-26
loaded via a namespace (and not attached):
[1] codetools_0.2-8 grid_2.14.0 nlme_3.1-101 splines_2.14.0 tools_2.14.0
Many thanks and apologies for lack of previous details.
Cheers
Chris
R 32-bit message when nlmer() crashes r.
Process: R [3850]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R for Mac OS X GUI 1.40-devel Leopard build 32-bit (5862)
Code Type: X86 (Native)
Parent Process: launchd [112]
Date/Time: 2011-06-29 09:13:06.737 +0200
OS Version: Mac OS X 10.6.8 (10K540)
Report Version: 6
Interval Since Last Report: 78981 sec
Crashes Since Last Report: 84
Per-App Interval Since Last Report: 1581 sec
Per-App Crashes Since Last Report: 1
Anonymous UUID: F882E507-864C-4DA4-BDFF-C104FBB881C2
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Application Specific Information:
abort() called
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libSystem.B.dylib 0x923b4c5a __kill + 10
1 libSystem.B.dylib 0x923b4c4c kill$UNIX2003 + 32
2 libSystem.B.dylib 0x924475a5 raise + 26
3 libSystem.B.dylib 0x9245d6e4 abort + 93
4 libstdc++.6.dylib 0x99ba4fda __gnu_cxx::__verbose_terminate_handler() + 433
5 libstdc++.6.dylib 0x99ba317a __cxxabiv1::__terminate(void (*)()) + 10
6 libstdc++.6.dylib 0x99ba31ba __cxxabiv1::__unexpected(void (*)()) + 0
7 libstdc++.6.dylib 0x99ba32b8 __gxx_exception_cleanup(_Unwind_Reason_Code, _Unwind_Exception*) + 0
8 minqa.so 0x27c54f00 calfun_ + 688
9 minqa.so 0x27c5a61f prelim_ + 863
10 minqa.so 0x27c50cc0 bobyqb_ + 272
11 minqa.so 0x27c50b1b bobyqa_ + 731
12 minqa.so 0x27c55ff5 bobyqa_cpp + 1029
13 libR.dylib 0x00124811 do_dotcall + 1009 (dotcode.c:856)
14 libR.dylib 0x00152ef1 Rf_eval + 1777 (eval.c:495)
15 libR.dylib 0x00156066 do_set + 678 (eval.c:1709)
16 libR.dylib 0x00152cf2 Rf_eval + 1266 (eval.c:469)
17 libR.dylib 0x001549c7 do_begin + 327 (eval.c:1407)
18 libR.dylib 0x00152cf2 Rf_eval + 1266 (eval.c:469)
19 libR.dylib 0x00157d31 Rf_applyClosure + 833 (eval.c:825)
20 libR.dylib 0x00152bf2 Rf_eval + 1010 (eval.c:513)
21 libR.dylib 0x00156066 do_set + 678 (eval.c:1709)
22 libR.dylib 0x00152cf2 Rf_eval + 1266 (eval.c:469)
23 libR.dylib 0x001549c7 do_begin + 327 (eval.c:1407)
24 libR.dylib 0x00152cf2 Rf_eval + 1266 (eval.c:469)
25 libR.dylib 0x00157d31 Rf_applyClosure + 833 (eval.c:825)
26 libR.dylib 0x00152bf2 Rf_eval + 1010 (eval.c:513)
27 libR.dylib 0x001549c7 do_begin + 327 (eval.c:1407)
28 libR.dylib 0x00152cf2 Rf_eval + 1266 (eval.c:469)
29 libR.dylib 0x00157d31 Rf_applyClosure + 833 (eval.c:825)
30 libR.dylib 0x00152bf2 Rf_eval + 1010 (eval.c:513)
31 libR.dylib 0x00156066 do_set + 678 (eval.c:1709)
32 libR.dylib 0x00152cf2 Rf_eval + 1266 (eval.c:469)
33 libR.dylib 0x0018dd51 R_ReplDLLdo1 + 513 (main.c:358)
34 org.R-project.R 0x0001f4ac run_REngineRmainloop + 252
35 org.R-project.R 0x0001474c -[REngine runREPL] + 284
36 org.R-project.R 0x00002600 main + 1024
37 org.R-project.R 0x00002046 start + 54
Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x9237a382 kevent + 10
1 libSystem.B.dylib 0x9237aa9c _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x92379f59 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x92379cfe _dispatch_worker_thread2 + 240
4 libSystem.B.dylib 0x92379781 _pthread_wqthread + 390
5 libSystem.B.dylib 0x923795c6 start_wqthread + 30
Thread 2:
0 libobjc.A.dylib 0x99a27fa0 objc_msgSend + 48
1 com.apple.Foundation 0x9046f352 -[NSDistantObject methodSignatureForSelector:] + 192
2 com.apple.CoreFoundation 0x9194a9c0 ___forwarding___ + 320
3 com.apple.CoreFoundation 0x9194a802 _CF_forwarding_prep_0 + 50
4 org.R-project.R 0x00011465 -[RController readThread:] + 2181
5 com.apple.Foundation 0x90417564 -[NSThread main] + 45
6 com.apple.Foundation 0x90417514 __NSThread__main__ + 1499
7 libSystem.B.dylib 0x92381259 _pthread_start + 345
8 libSystem.B.dylib 0x923810de thread_start + 34
Thread 3: com.apple.CFSocket.private
0 libSystem.B.dylib 0x92372ac6 select$DARWIN_EXTSN + 10
1 com.apple.CoreFoundation 0x9194cc83 __CFSocketManager + 1091
2 libSystem.B.dylib 0x92381259 _pthread_start + 345
3 libSystem.B.dylib 0x923810de thread_start + 34
Thread 4:
0 libSystem.B.dylib 0x92353afa mach_msg_trap + 10
1 libSystem.B.dylib 0x92354267 mach_msg + 68
2 com.apple.CoreFoundation 0x9190d30f __CFRunLoopRun + 2079
3 com.apple.CoreFoundation 0x9190c3f4 CFRunLoopRunSpecific + 452
4 com.apple.CoreFoundation 0x9190c221 CFRunLoopRunInMode + 97
5 com.apple.Foundation 0x904502c4 +[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] + 329
6 com.apple.Foundation 0x90417564 -[NSThread main] + 45
7 com.apple.Foundation 0x90417514 __NSThread__main__ + 1499
8 libSystem.B.dylib 0x92381259 _pthread_start + 345
9 libSystem.B.dylib 0x923810de thread_start + 34
Thread 5:
0 libSystem.B.dylib 0x92379412 __workq_kernreturn + 10
1 libSystem.B.dylib 0x923799a8 _pthread_wqthread + 941
2 libSystem.B.dylib 0x923795c6 start_wqthread + 30
Thread 6:
0 libSystem.B.dylib 0x92379412 __workq_kernreturn + 10
1 libSystem.B.dylib 0x923799a8 _pthread_wqthread + 941
2 libSystem.B.dylib 0x923795c6 start_wqthread + 30
Thread 7:
0 libSystem.B.dylib 0x92379412 __workq_kernreturn + 10
1 libSystem.B.dylib 0x923799a8 _pthread_wqthread + 941
2 libSystem.B.dylib 0x923795c6 start_wqthread + 30
Thread 8:
0 libSystem.B.dylib 0x92381aa2 __semwait_signal + 10
1 libSystem.B.dylib 0x923ad9c5 nanosleep$UNIX2003 + 188
2 libSystem.B.dylib 0x923ad903 usleep$UNIX2003 + 61
3 com.apple.AppKit 0x95b52e2d -[NSUIHeartBeat _heartBeatThread:] + 2039
4 com.apple.Foundation 0x90417564 -[NSThread main] + 45
5 com.apple.Foundation 0x90417514 __NSThread__main__ + 1499
6 libSystem.B.dylib 0x92381259 _pthread_start + 345
7 libSystem.B.dylib 0x923810de thread_start + 34
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0x9245d693 ecx: 0xbfffdd1c edx: 0x923b4c5a
edi: 0xa02d4b30 esi: 0x251b4b4c ebp: 0xbfffdd38 esp: 0xbfffdd1c
ss: 0x0000001f efl: 0x00000282 eip: 0x923b4c5a cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0xa02e6020
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Model: iMac8,1, BootROM IM81.00C1.B00, 2 processors, Intel Core 2 Duo, 3.06 GHz, 2 GB, SMC 1.30f1
Graphics: NVIDIA GeForce 8800 GS, NVIDIA GeForce 8800 GS, PCIe, 512 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8C), Broadcom BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Serial ATA Device: WDC WD5000AAKS-40YGA1, 465.76 GB
Parallel ATA Device: MATSHITADVD-R UJ-875
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8502, 0xfd400000 / 2
USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1006, 0xfa200000 / 2
USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x0221, 0xfa220000 / 3
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x1a100000 / 2
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x820f, 0x1a110000 / 3
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x5d100000 / 2
FireWire Device: Rugged FW/USB, LaCie, Up to 800 Mb/sec
On 26 Jun 2011, at 21:59, Ben Bolker wrote:
On 11-06-27 11:57 AM, Christopher Philipson wrote:
Dear mixed modelers, I am running r 2.13 and have installed lme4a. When I try my nlmer model (that works in lme4) r crashes. I am running mac osx 10.6.7 Any ideas?
More details (especially including a reproducible example) would be very helpful ... see e.g. https://gist.github.com/270442 ... Ben Bolker
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
Dr. Christopher Philipson Institute of Evolutionary Biology and Environmental Studies, Winterthuerstrasse 190, CH-8057, Zurich Tel: 00 41 44 635 61 29 Fax: 00 41 44 635 57 11 christopher.philipson at ieu.uzh.ch
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