I was trying to install OMERO using the instructions in
http://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html
I was originally using Enthought's python and it failed. Now I know that you should not install packages using brew in a virtual enviroment which is essentially what Enthought Canopy is. So I removed that and then I removed MacPorts and proceeded to install brew and follow the instructions in the page.
And I get the following error. Tried erasing and starting again but I still get the same error.
I essentially get a message
- Code: Select all
jenkins:bin icaoberg$ omero shell
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
and the error that it wants to send to Apple which I pasted below. Feedback would be deeply appreciated.
Process: Python [26984]
Path: /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.5 (2.7.5)
Code Type: X86-64 (Native)
Parent Process: bash [31735]
User ID: 501
Date/Time: 2013-11-05 13:43:31.349 -0500
OS Version: Mac OS X 10.8.5 (12F45)
Report Version: 10
Interval Since Last Report: 78875 sec
Crashes Since Last Report: 1
Per-App Crashes Since Last Report: 1
Anonymous UUID: A46820FE-F6AF-0846-61E8-C9AECE847B8A
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Application Specific Information:
abort() called
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff8ea3bd46 __kill + 10
1 libsystem_c.dylib 0x00007fff8ce4af83 abort + 177
2 org.python.python 0x0000000100d91eaa Py_FatalError + 49
3 org.python.python 0x0000000100d90370 PyThreadState_Get + 28
4 org.python.python 0x0000000100d8bf16 Py_InitModule4_64 + 58
5 IcePy.so 0x00000001007ce31e initIcePy + 45
6 org.python.python 0x000000010032ddb9 _PyImport_LoadDynamicModule + 150
7 org.python.python 0x000000010032dad0 import_submodule + 274
8 org.python.python 0x000000010032d6aa load_next + 277
9 org.python.python 0x000000010032b9b9 PyImport_ImportModuleLevel + 1151
10 org.python.python 0x00000001003118c7 builtin___import__ + 132
11 org.python.python 0x000000010029fdcd PyObject_Call + 101
12 org.python.python 0x000000010031c1c4 PyEval_CallObjectWithKeywords + 93
13 org.python.python 0x00000001003193f9 PyEval_EvalFrameEx + 12527
14 org.python.python 0x00000001003161e0 PyEval_EvalCodeEx + 1638
15 org.python.python 0x0000000100315b74 PyEval_EvalCode + 54
16 org.python.python 0x000000010032a555 PyImport_ExecCodeModuleEx + 247
17 org.python.python 0x000000010032d084 load_source_module + 1068
18 org.python.python 0x000000010032dad0 import_submodule + 274
19 org.python.python 0x000000010032d6e8 load_next + 339
20 org.python.python 0x000000010032b9b9 PyImport_ImportModuleLevel + 1151
21 org.python.python 0x00000001003118c7 builtin___import__ + 132
22 org.python.python 0x000000010029fdcd PyObject_Call + 101
23 org.python.python 0x000000010031c1c4 PyEval_CallObjectWithKeywords + 93
24 org.python.python 0x00000001003193f9 PyEval_EvalFrameEx + 12527
25 org.python.python 0x00000001003161e0 PyEval_EvalCodeEx + 1638
26 org.python.python 0x0000000100315b74 PyEval_EvalCode + 54
27 org.python.python 0x000000010032a555 PyImport_ExecCodeModuleEx + 247
28 org.python.python 0x000000010032d084 load_source_module + 1068
29 org.python.python 0x000000010032d300 load_package + 298
30 org.python.python 0x000000010032dad0 import_submodule + 274
31 org.python.python 0x000000010032d6aa load_next + 277
32 org.python.python 0x000000010032b9b9 PyImport_ImportModuleLevel + 1151
33 org.python.python 0x00000001003118c7 builtin___import__ + 132
34 org.python.python 0x000000010029fdcd PyObject_Call + 101
35 org.python.python 0x000000010031c1c4 PyEval_CallObjectWithKeywords + 93
36 org.python.python 0x00000001003193f9 PyEval_EvalFrameEx + 12527
37 org.python.python 0x00000001003161e0 PyEval_EvalCodeEx + 1638
38 org.python.python 0x0000000100315b74 PyEval_EvalCode + 54
39 org.python.python 0x0000000100335040 run_mod + 53
40 org.python.python 0x00000001003350e7 PyRun_FileExFlags + 137
41 org.python.python 0x0000000100334c35 PyRun_SimpleFileExFlags + 718
42 org.python.python 0x0000000100345677 Py_Main + 2995
43 libdyld.dylib 0x00007fff8c0e57e1 start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00007fff5f96d400 rcx: 0x00007fff5f96d3e8 rdx: 0x0000000000000000
rdi: 0x0000000000006968 rsi: 0x0000000000000006 rbp: 0x00007fff5f96d410 rsp: 0x00007fff5f96d3e8
r8: 0x00000000000003f5 r9: 0x00007fff5f96d630 r10: 0x00007fff8ea3d342 r11: 0x0000000000000202
r12: 0x0000000000000000 r13: 0x000000010082ee02 r14: 0x00000000000003f5 r15: 0x0000000000000000
rip: 0x00007fff8ea3bd46 rfl: 0x0000000000000202 cr2: 0x00007fff73ecfff0
Logical CPU: 0
Binary Images:
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0x100296000 - 0x1003a0ff7 +org.python.python (2.7.5, [c] 2004-2013 Python Software Foundation. - 2.7.5) <D8F4D662-0578-3882-8C75-CFF2C8214091> /usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/Python
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0x1007bf000 - 0x100844fff +IcePy.so (0) <BAEFE456-90A4-381D-811C-59D45E3DB527> /usr/local/Cellar/omero/4.4.9/lib/python/IcePy.so
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0x7fff5fe91000 - 0x7fff5fec593f dyld (210.2.3) <6900F2BA-DB48-3B78-B668-58FC0CF6BCB8> /usr/lib/dyld
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0x7fff82fb5000 - 0x7fff82fcaff7 libdispatch.dylib (228.23) <D26996BF-FC57-39EB-8829-F63585561E09> /usr/lib/system/libdispatch.dylib
0x7fff830c9000 - 0x7fff830d6fff libbz2.1.0.dylib (29) <CE9785E8-B535-3504-B392-82F0064D9AF2> /usr/lib/libbz2.1.0.dylib
0x7fff83272000 - 0x7fff83297ff7 libc++abi.dylib (26) <D86169F3-9F31-377A-9AF3-DB17142052E4> /usr/lib/libc++abi.dylib
0x7fff8396a000 - 0x7fff8396afff libkeymgr.dylib (25) <CC9E3394-BE16-397F-926B-E579B60EE429> /usr/lib/system/libkeymgr.dylib
0x7fff83e80000 - 0x7fff84080fff libicucore.A.dylib (491.11.3) <5783D305-04E8-3D17-94F7-1CEAFA975240> /usr/lib/libicucore.A.dylib
0x7fff840b7000 - 0x7fff840b8ff7 libdnsinfo.dylib (453.19) <14202FFB-C3CA-3FCC-94B0-14611BF8692D> /usr/lib/system/libdnsinfo.dylib
0x7fff8535d000 - 0x7fff853acff7 libcorecrypto.dylib (106.2) <CE0C29A3-C420-339B-ADAA-52F4683233CC> /usr/lib/system/libcorecrypto.dylib
0x7fff853ad000 - 0x7fff853aeff7 libsystem_sandbox.dylib (220.3) <B739DA63-B675-387A-AD84-412A651143C0> /usr/lib/system/libsystem_sandbox.dylib
0x7fff8606d000 - 0x7fff86257ff7 com.apple.CoreFoundation (6.8 - 744.19) <0F7403CA-2CB8-3D0A-992B-679701DF27CA> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff87d11000 - 0x7fff87d1cfff libsystem_notify.dylib (98.5) <C49275CC-835A-3207-AFBA-8C01374927B6> /usr/lib/system/libsystem_notify.dylib
0x7fff88bae000 - 0x7fff88baffff libsystem_blocks.dylib (59) <D92DCBC3-541C-37BD-AADE-ACC75A0C59C8> /usr/lib/system/libsystem_blocks.dylib
0x7fff88eb2000 - 0x7fff88eb3fff libDiagnosticMessagesClient.dylib (8) <8548E0DC-0D2F-30B6-B045-FE8A038E76D8> /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff8b175000 - 0x7fff8b17bfff libmacho.dylib (829) <BF332AD9-E89F-387E-92A4-6E1AB74BD4D9> /usr/lib/system/libmacho.dylib
0x7fff8c0e3000 - 0x7fff8c0e6ff7 libdyld.dylib (210.2.3) <F59367C9-C110-382B-A695-9035A6DD387E> /usr/lib/system/libdyld.dylib
0x7fff8cc3d000 - 0x7fff8cc4bfff libcommonCrypto.dylib (60027) <BAAFE0C9-BB86-3CA7-88C0-E3CBA98DA06F> /usr/lib/system/libcommonCrypto.dylib
0x7fff8cc97000 - 0x7fff8cce3ff7 libauto.dylib (185.4) <AD5A4CE7-CB53-313C-9FAE-673303CC2D35> /usr/lib/libauto.dylib
0x7fff8cdf1000 - 0x7fff8cebdff7 libsystem_c.dylib (825.40.1) <543B05AE-CFA5-3EFE-8E58-77225411BA6B> /usr/lib/system/libsystem_c.dylib
0x7fff8d244000 - 0x7fff8d246ff7 libunc.dylib (25) <92805328-CD36-34FF-9436-571AB0485072> /usr/lib/system/libunc.dylib
0x7fff8d31c000 - 0x7fff8d385fff libstdc++.6.dylib (56) <EAA2B53E-EADE-39CF-A0EF-FB9D4940672A> /usr/lib/libstdc++.6.dylib
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0x7fff8dc74000 - 0x7fff8dc7bfff libcopyfile.dylib (89) <876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib
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0x7fff8ec50000 - 0x7fff8ec72ff7 libxpc.dylib (140.43) <70BC645B-6952-3264-930C-C835010CCEF9> /usr/lib/system/libxpc.dylib
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0x7fff8ef29000 - 0x7fff8ef91ff7 libc++.1.dylib (65.1) <20E31B90-19B9-3C2A-A9EB-474E08F9FE05> /usr/lib/libc++.1.dylib
0x7fff8f10e000 - 0x7fff8f114ff7 libunwind.dylib (35.1) <21703D36-2DAB-3D8B-8442-EAAB23C060D3> /usr/lib/system/libunwind.dylib
0x7fff8f462000 - 0x7fff8f464fff libquarantine.dylib (52.1) <143B726E-DF47-37A8-90AA-F059CFD1A2E4> /usr/lib/system/libquarantine.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
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: 9904
thread_create: 1
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=70.1M resident=50.9M(73%) swapped_out_or_unallocated=19.2M(27%)
Writable regions: Total=22.3M written=4564K(20%) resident=5440K(24%) swapped_out=0K(0%) unallocated=17.0M(76%)
REGION TYPE VIRTUAL
=========== =======
MALLOC 13.3M
MALLOC guard page 32K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 4K
__DATA 2524K
__LINKEDIT 54.5M
__TEXT 15.6M
__UNICODE 544K
shared memory 12K
=========== =======
TOTAL 150.4M
Model: Macmini6,2, BootROM MM61.0106.B03, 4 processors, Intel Core i7, 2.3 GHz, 16 GB, SMC 2.8f0
Graphics: Intel HD Graphics 4000, Intel HD Graphics 4000, Built-In, 768 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x029E, 0x434D5358384758334D314131363030433130
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x029E, 0x434D5358384758334D314131363030433130
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x10E), Broadcom BCM43xx 1.0 (5.106.98.100.17)
Bluetooth: Version 4.1.7f2 12718, 3 service, 21 devices, 3 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Serial ATA Device: APPLE HDD HTS541010A9E662, 1 TB
USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1a100000 / 2
USB Device: hub_device, 0x8087 (Intel Corporation), 0x0024, 0x1d100000 / 2
USB Device: hub_device, 0x0424 (SMSC), 0x2512, 0x1d180000 / 3
USB Device: IR Receiver, apple_vendor_id, 0x8242, 0x1d182000 / 5
USB Device: BRCM20702 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x1d181000 / 4
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x828a, 0x1d181300 / 8
USB Device: Trackball, 0x046d (Logitech Inc.), 0xc404, 0x14400000 / 2
USB Device: USB Receiver, 0x046d (Logitech Inc.), 0xc52b, 0x14100000 / 1
