[R-sig-ME] lme4a crash
Christopher Philipson
christopher.philipson at ieu.uzh.ch
Wed Jun 29 09:24:12 CEST 2011
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
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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0x99894000 - 0x998ccfe7 libncurses.5.4.dylib 5.4.0 (compatibility 5.4.0) <8776C654-D54E-9756-A58D-74738A4E9497> /usr/lib/libncurses.5.4.dylib
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0x998db000 - 0x99978fe3 com.apple.LaunchServices 362.3 (362.3) <15B47388-16C8-97DA-EEBB-1709E136169E> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
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0x99ad3000 - 0x99b09fff libtidy.A.dylib ??? (???) <0FD72C68-4803-4C5B-3A63-05D7394BFD71> /usr/lib/libtidy.A.dylib
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0xffff0000 - 0xffff1fff libSystem.B.dylib ??? (???) <2DCD13E3-1BD1-6F25-119A-3863A3848B90> /usr/lib/libSystem.B.dylib
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:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
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> 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
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> _______________________________________________
> 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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