[R-SIG-Mac] R.app crashes on Mac OSX 10.10.3
Peter Baker
baker.peter2009 at gmail.com
Wed May 20 07:22:40 CEST 2015
Hi All
Very sorry to bother you but I talked my Uni into getting me a MacBook so I
can help students with R. While I've been using unix, linux and windows for
about 25 years I haven't used a Mac before
I have access as a local administrator but not as root which is reserved
for ITS sysadmins. Could this be the problem why R.app crashes?
> sessionInfo()
R version 3.2.0 Patched (2015-05-13 r68368)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.2.0 tools_3.2.0
>
I get the same problem whether I try to run R-3.2.0, R-patched, and R-devel
R seems to run fine in terminal, RStudio and emacs ESS but not from R.app
After trying the three available binary packages, I compiled from source
but even as a local administrator I can't install it which makes me think
it is a permissions problem
Xcode 6.3.1, gfortran 4.9.2 although App Store suggested upgrading Xcode
Any hints would be greatfully appreciated. Thanks!
Regards
Peter
============================================================
Process: R [1124]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R for Mac OS X GUI 1.66-devel Mavericks build (6941)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: R [1124]
User ID: 1129002265
Date/Time: 2015-05-17 20:54:44.740 +1000
OS Version: Mac OS X 10.10.3 (14D136)
Report Version: 11
Anonymous UUID: 4D5CC913-8F07-619E-DBDD-E9E366AC1FA7
Sleep/Wake UUID: A3BF7197-653C-49D9-B12B-6241F3D1007C
Time Awake Since Boot: 110000 seconds
Time Since Wake: 6600 seconds
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Application Specific Information:
*** Terminating app due to uncaught exception 'NSInvalidArgumentException',
reason: '*** -[__NSArrayM insertObject:atIndex:]: object cannot be nil'
abort() called
terminating with uncaught exception of type NSException
Application Specific Backtrace 1:
0 CoreFoundation 0x00007fff9922803c
__exceptionPreprocess + 172
1 libobjc.A.dylib 0x00007fff9946b76e
objc_exception_throw + 43
2 CoreFoundation 0x00007fff990d3329 -[__NSArrayM
insertObject:atIndex:] + 1033
3 AppKit 0x00007fff92c7f0b3 -[NSColorPanel
_provideNewViewFor:initialViewRequest:] + 91
4 AppKit 0x00007fff92c82fcc -[NSColorPanel
_switchToPicker:] + 127
5 AppKit 0x00007fff92c7effc -[NSColorPanel
setMode:] + 424
6 AppKit 0x00007fff92c812dd -[NSColorPanel
_constructWithPickers:] + 1163
7 AppKit 0x00007fff92c7da1d -[NSColorPanel
initWithContentRect:styleMask:backing:defer:] + 916
8 AppKit 0x00007fff929d682a -[NSPanel init]
+ 87
9 R 0x000000010115cef5 -[ColorsPrefPane
awakeFromNib] + 85
10 CoreFoundation 0x00007fff99134bdf -[NSSet
makeObjectsPerformSelector:] + 223
11 AppKit 0x00007fff927ad14d -[NSIBObjectData
nibInstantiateWithOwner:options:topLevelObjects:] + 1216
12 AppKit 0x00007fff9278c205 loadNib + 384
13 AppKit 0x00007fff9278b72b
+[NSBundle(NSNibLoading)
_loadNibFile:nameTable:options:withZone:ownerBundle:] + 313
14 AppKit 0x00007fff9278b4e7
-[NSBundle(NSNibLoading) loadNibNamed:owner:topLevelObjects:] + 201
15 AppKit 0x00007fff9278b2b3
+[NSBundle(NSNibLoading) loadNibNamed:owner:] + 344
16 R 0x000000010115d1a7 -[ColorsPrefPane
mainView] + 55
17 R 0x0000000101158629
-[AMPreferenceWindowController addPane:withIdentifier:] + 201
18 R 0x00000001011608ab
-[PrefWindowController awakeFromNib] + 667
19 CoreFoundation 0x00007fff99134bdf -[NSSet
makeObjectsPerformSelector:] + 223
20 AppKit 0x00007fff927ad14d -[NSIBObjectData
nibInstantiateWithOwner:options:topLevelObjects:] + 1216
21 AppKit 0x00007fff9278c205 loadNib + 384
22 AppKit 0x00007fff9278b72b
+[NSBundle(NSNibLoading)
_loadNibFile:nameTable:options:withZone:ownerBundle:] + 313
23 AppKit 0x00007fff9278b4e7
-[NSBundle(NSNibLoading) loadNibNamed:owner:topLevelObjects:] + 201
24 AppKit 0x00007fff9278b2b3
+[NSBundle(NSNibLoading) loadNibNamed:owner:] + 344
25 R 0x0000000101130d8e main + 366
26 libdyld.dylib 0x00007fff98ffb5c9 start + 1
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff9441c286 __pthread_kill + 10
1 libsystem_c.dylib 0x00007fff91d68b53 abort + 129
2 libc++abi.dylib 0x00007fff8ea79a21 abort_message + 257
3 libc++abi.dylib 0x00007fff8eaa19d1
default_terminate_handler() + 267
4 libobjc.A.dylib 0x00007fff9946f7d6 _objc_terminate()
+ 103
5 libc++abi.dylib 0x00007fff8ea9f0a1
std::__terminate(void (*)()) + 8
6 libc++abi.dylib 0x00007fff8ea9eb30 __cxa_throw + 121
7 libobjc.A.dylib 0x00007fff9946b898
objc_exception_throw + 341
8 com.apple.CoreFoundation 0x00007fff990d3329 -[__NSArrayM
insertObject:atIndex:] + 1033
9 com.apple.AppKit 0x00007fff92c7f0b3 -[NSColorPanel
_provideNewViewFor:initialViewRequest:] + 91
10 com.apple.AppKit 0x00007fff92c82fcc -[NSColorPanel
_switchToPicker:] + 127
11 com.apple.AppKit 0x00007fff92c7effc -[NSColorPanel
setMode:] + 424
12 com.apple.AppKit 0x00007fff92c812dd -[NSColorPanel
_constructWithPickers:] + 1163
13 com.apple.AppKit 0x00007fff92c7da1d -[NSColorPanel
initWithContentRect:styleMask:backing:defer:] + 916
14 com.apple.AppKit 0x00007fff929d682a -[NSPanel init] +
87
15 org.R-project.R 0x000000010115cef5 -[ColorsPrefPane
awakeFromNib] + 85
16 com.apple.CoreFoundation 0x00007fff99134bdf -[NSSet
makeObjectsPerformSelector:] + 223
17 com.apple.AppKit 0x00007fff927ad14d -[NSIBObjectData
nibInstantiateWithOwner:options:topLevelObjects:] + 1216
18 com.apple.AppKit 0x00007fff9278c205 loadNib + 384
19 com.apple.AppKit 0x00007fff9278b72b
+[NSBundle(NSNibLoading)
_loadNibFile:nameTable:options:withZone:ownerBundle:] + 313
20 com.apple.AppKit 0x00007fff9278b4e7
-[NSBundle(NSNibLoading) loadNibNamed:owner:topLevelObjects:] + 201
21 com.apple.AppKit 0x00007fff9278b2b3
+[NSBundle(NSNibLoading) loadNibNamed:owner:] + 344
22 org.R-project.R 0x000000010115d1a7 -[ColorsPrefPane
mainView] + 55
23 org.R-project.R 0x0000000101158629
-[AMPreferenceWindowController addPane:withIdentifier:] + 201
24 org.R-project.R 0x00000001011608ab
-[PrefWindowController awakeFromNib] + 667
25 com.apple.CoreFoundation 0x00007fff99134bdf -[NSSet
makeObjectsPerformSelector:] + 223
26 com.apple.AppKit 0x00007fff927ad14d -[NSIBObjectData
nibInstantiateWithOwner:options:topLevelObjects:] + 1216
27 com.apple.AppKit 0x00007fff9278c205 loadNib + 384
28 com.apple.AppKit 0x00007fff9278b72b
+[NSBundle(NSNibLoading)
_loadNibFile:nameTable:options:withZone:ownerBundle:] + 313
29 com.apple.AppKit 0x00007fff9278b4e7
-[NSBundle(NSNibLoading) loadNibNamed:owner:topLevelObjects:] + 201
30 com.apple.AppKit 0x00007fff9278b2b3
+[NSBundle(NSNibLoading) loadNibNamed:owner:] + 344
31 org.R-project.R 0x0000000101130d8e main + 366
32 libdyld.dylib 0x00007fff98ffb5c9 start + 1
Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff9441d232 kevent64 + 10
1 libdispatch.dylib 0x00007fff9a410a6a
_dispatch_mgr_thread + 52
Thread 2:
0 libsystem_kernel.dylib 0x00007fff9441c94a __workq_kernreturn
+ 10
1 libsystem_pthread.dylib 0x00007fff8f68040d start_wqthread + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff9441c94a __workq_kernreturn
+ 10
1 libsystem_pthread.dylib 0x00007fff8f68040d start_wqthread + 13
Thread 4:
0 libsystem_kernel.dylib 0x00007fff9441c94a __workq_kernreturn
+ 10
1 libsystem_pthread.dylib 0x00007fff8f68040d start_wqthread + 13
Thread 5:
0 libsystem_kernel.dylib 0x00007fff9441c94a __workq_kernreturn
+ 10
1 libsystem_pthread.dylib 0x00007fff8f68040d start_wqthread + 13
Thread 6:
0 libsystem_kernel.dylib 0x00007fff944174de mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff9441664f mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff99136eb4
__CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff9913637b __CFRunLoopRun +
1371
4 com.apple.CoreFoundation 0x00007fff99135bd8
CFRunLoopRunSpecific + 296
5 com.apple.Foundation 0x00007fff95195d2c -[NSConnection
sendInvocation:internal:] + 2095
6 com.apple.CoreFoundation 0x00007fff99170c26 ___forwarding___ +
518
7 com.apple.CoreFoundation 0x00007fff99170998
_CF_forwarding_prep_0 + 120
8 com.apple.Foundation 0x00007fff9519462e -[NSConnection
rootProxy] + 68
9 org.R-project.R 0x00000001011339e3 -[RController
readThread:] + 179
10 com.apple.Foundation 0x00007fff9511ddc2 __NSThread__main__
+ 1345
11 libsystem_pthread.dylib 0x00007fff8f682268 _pthread_body + 131
12 libsystem_pthread.dylib 0x00007fff8f6821e5 _pthread_start +
176
13 libsystem_pthread.dylib 0x00007fff8f68041d thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx:
0x00007fff5eace5d8 rdx: 0x0000000000000000
rdi: 0x000000000000130f rsi: 0x0000000000000006 rbp:
0x00007fff5eace600 rsp: 0x00007fff5eace5d8
r8: 0x6e6f697470656378 r9: 0x00007fff91d92d70 r10:
0x0000000008000000 r11: 0x0000000000000206
r12: 0x00007fff5eace760 r13: 0x00007fb4b2f02970 r14:
0x00007fff7dc9e300 r15: 0x00007fff5eace640
rip: 0x00007fff9441c286 rfl: 0x0000000000000206 cr2: 0x00007fff7e0b2fd8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff9cc0f000 - 0x7fff9cef6ffb com.apple.CoreServices.CarbonCore
(1108.6 - 1108.6) <8953580E-7857-33B2-AA64-98296830D3A8>
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
0x7fff9d02d000 - 0x7fff9d02dfff com.apple.quartzframework (1.5 -
1.5) <26C982A3-2FC3-3F50-B5F4-3C545C3BAC10>
/System/Library/Frameworks/Quartz.framework/Versions/A/Quartz
0x7fff9d0c6000 - 0x7fff9d0fefff libsystem_network.dylib (412.20.3)
<589A5F67-BE2A-3245-A181-0ECC9B53EB00>
/usr/lib/system/libsystem_network.dylib
0x7fff9d0ff000 - 0x7fff9d101fff com.apple.SecCodeWrapper (4.0 -
238.20.2) <C6C126F0-6BF4-3E29-A9B7-7BAD8D17EE4F>
/System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff9d102000 - 0x7fff9d404ffb com.apple.GeoServices (1.0 -
1077.0.18) <2BBF8B44-DD46-3432-8C84-6D6AA004C233>
/System/Library/PrivateFrameworks/GeoServices.framework/Versions/A/GeoServices
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 1
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 68081
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=241.1M resident=155.1M(64%)
swapped_out_or_unallocated=86.0M(36%)
Writable regions: Total=1.1G written=6020K(1%) resident=8988K(1%)
swapped_out=0K(0%) unallocated=1.1G(99%)
REGION TYPE VIRTUAL
=========== =======
CG image 392K
CG shared images 176K
CoreUI image data 4K
Image IO 84K
JS JIT generated code 8K
JS JIT generated code (reserved) 1.0G reserved VM address space
(unallocated)
Kernel Alloc Once 8K
MALLOC 49.1M
MALLOC (admin) 32K
Memory Tag 251 16K
STACK GUARD 56.0M
Stack 10.6M
VM_ALLOCATE 1180K
WebKit Malloc 728K
__DATA 23.2M
__IMAGE 528K
__LINKEDIT 72.2M
__TEXT 168.8M
__UNICODE 552K
mapped file 66.2M
shared memory 4K
=========== =======
TOTAL 1.4G
TOTAL, minus reserved VM space 449.8M
Model: MacBookPro12,1, BootROM MBP121.0167.B02, 2 processors, Intel Core
i7, 3.1 GHz, 16 GB, SMC 2.28f6
Graphics: Intel Iris Graphics 6100, Intel Iris Graphics 6100, Built-In
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1867 MHz, 0x02FE,
0x4544464232333241314D412D4A442D460000
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1867 MHz, 0x02FE,
0x4544464232333241314D412D4A442D460000
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x133),
Broadcom BCM43xx 1.0 (7.15.166.24.3)
Bluetooth: Version 4.3.4f4 15601, 3 services, 18 devices, 1 incoming serial
ports
Network Service: Thunderbolt Ethernet, Ethernet, en3
PCI Card: Apple 57762-A0, Ethernet Controller, Thunderbolt at 195,0,0
Serial ATA Device: APPLE SSD SM0512G, 500.28 GB
USB Device: Internal Memory Card Reader
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1
Thunderbolt Device: Thunderbolt to Gigabit Ethernet Adapter, Apple Inc., 1,
5.5
--
Dr Peter Baker | Senior Lecturer/Statistician | Epidemiology & Biostatistics
Room 233 | School of Population Health |The University of Queensland |
Public
Health Building | Herston Rd | Herston Qld 4006 | Australia
Ph: +61 7 3346 4747 | Fax: +61 7 3365 5442 | http://www.sph.uq.edu.au/ |
Email: p.baker1 at uq.edu.au or baker.peter2009 at gmail.com
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