Installing OMERO in MacOSX using homebrew
Posted: Tue Nov 05, 2013 6:55 pmHi!
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
and the error that it wants to send to Apple which I pasted below. Feedback would be deeply appreciated.
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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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