Open Microscopy Environment

Posted: **Thu Feb 02, 2017 5:36 am**

Upgrading OMERO server to version 2.7 on Apple platform, I had been running previous version all last year.

I get the following message along with BUILD FAILED

It looks like it cannot find jgoodies-common;1.7.0!jgoodies-common.jar

Any help?

Mark

digitalembryo:~ markhill$ brew install omero52 --with-nginx --with-cpp
==> Installing omero52 from ome/alt
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://downloads.openmicroscopy.org/ome ... cts/openmi
Already downloaded: /Users/markhill/Library/Caches/Homebrew/omero52-5.2.7.zip
==> ./build.py -Dice.home=/usr/local/opt/zeroc-ice35 build-all
Last 15 lines from /Users/markhill/Library/Logs/Homebrew/omero52/01.build.py:
:: com.jgoodies#jgoodies-common;1.7.0!jgoodies-common.jar
::::::::::::::::::::::::::::::::::::::::::::::

:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS

BUILD FAILED
/private/tmp/omero52-20170202-4172-8nrwmw/openmicroscopy-5.2.7/build.xml:189: The following error occurred while executing this line:
/private/tmp/omero52-20170202-4172-8nrwmw/openmicroscopy-5.2.7/components/antlib/resources/global.xml:430: The following error occurred while executing this line:
/private/tmp/omero52-20170202-4172-8nrwmw/openmicroscopy-5.2.7/components/tools/build.xml:28: The following error occurred while executing this line:
/private/tmp/omero52-20170202-4172-8nrwmw/openmicroscopy-5.2.7/components/antlib/resources/global.xml:430: The following error occurred while executing this line:
/private/tmp/omero52-20170202-4172-8nrwmw/openmicroscopy-5.2.7/components/antlib/resources/lifecycle.xml:67: impossible to resolve dependencies:
resolve failed - see output for details

Total time: 9 minutes 0 seconds

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/ome/homebrew-alt/issues

digitalembryo:~ markhill$

Posted: **Thu Feb 02, 2017 10:36 am**

Hi Mark,

This appears to be a failure to retrieve dependencies.

Have you tried a second time?

Last 15 lines from /Users/markhill/Library/Logs/Homebrew/omero52/01.build.py:

It would be worth sending us the full log if re-trying is the same.

Best,

Kenny

Posted: **Thu Feb 02, 2017 11:21 pm**

Hi Kenny,

Yes tried a few times Here's todays, I think they have moved the web location for 1.7.0!jgoodies-common.jar, if I knew where I should put the JAR file I could place it locally. M

🍺 /usr/local/Cellar/nginx/1.10.3: 8 files, 980.9K
==> Installing ome/alt/omero52 --with-cpp --with-nginx
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://downloads.openmicroscopy.org/ome ... cts/openmi
Already downloaded: /Users/markhill/Library/Caches/Homebrew/omero52-5.2.7.zip
==> ./build.py -Dice.home=/usr/local/opt/zeroc-ice35 build-all
Last 15 lines from /Users/markhill/Library/Logs/Homebrew/omero52/01.build.py:
:: com.jgoodies#jgoodies-common;1.7.0!jgoodies-common.jar
::::::::::::::::::::::::::::::::::::::::::::::

:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS

BUILD FAILED
/private/tmp/omero52-20170203-36784-15f4rk5/openmicroscopy-5.2.7/build.xml:189: The following error occurred while executing this line:
/private/tmp/omero52-20170203-36784-15f4rk5/openmicroscopy-5.2.7/components/antlib/resources/global.xml:430: The following error occurred while executing this line:
/private/tmp/omero52-20170203-36784-15f4rk5/openmicroscopy-5.2.7/components/tools/build.xml:28: The following error occurred while executing this line:
/private/tmp/omero52-20170203-36784-15f4rk5/openmicroscopy-5.2.7/components/antlib/resources/global.xml:430: The following error occurred while executing this line:
/private/tmp/omero52-20170203-36784-15f4rk5/openmicroscopy-5.2.7/components/antlib/resources/lifecycle.xml:67: impossible to resolve dependencies:
resolve failed - see output for details

Total time: 9 minutes 0 seconds

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/ome/homebrew-alt/issues

digitalembryo:~ markhill$

Posted: **Fri Feb 03, 2017 10:42 am**

Hi Mark,

Test there is no stale cache hanging around, you could try the following:

Code: Select all: `rm -rf ~/.m2/repository/com/jgoodies && brew install omero52 --with-nginx --with-cpp`

If you're still having problems, could you please send us the full log file?

Code: Select all: /Users/markhill/Library/Logs/Homebrew/omero52/01.build.py

Best,

Kenny

Posted: **Wed Feb 08, 2017 6:26 am**

Hi Kenny,

Thanks for the input, I've been able to complete the installation however I'm receiving a perplexing python error

Python quit unexpectedly while using the Python plug-in.

when executing

Code: Select all: omero web start

My OMERO diagnostics output is as follows:

================================================================================
OMERO Diagnostics 5.2.7-ice35
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.13 (/usr/local/bin/python -- 2 others)
Commands: icegridnode --version 3.5.1 (/usr/local/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/local/bin/icegridadmin)
Commands: psql --version 9.4.9 (/usr/local/bin/psql -- 2 others)

Server: icegridnode running
Server: Blitz-0 active (pid = 19492, enabled)
Server: DropBox active (pid = 19493, enabled)
Server: FileServer active (pid = 19494, enabled)
Server: Indexer-0 active (pid = 19495, enabled)
Server: MonitorServer active (pid = 19496, enabled)
Server: OMERO.Glacier2 active (pid = 19497, enabled)
Server: OMERO.IceStorm active (pid = 19498, enabled)
Server: PixelData-0 active (pid = 19499, enabled)
Server: Processor-0 active (pid = 19500, enabled)
Server: Tables-0 active (pid = 19501, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /usr/local/Cellar/omero52/5.2.7/var/log exists
Log files: Blitz-0.log 4.0 MB errors=213 warnings=5
Log files: DropBox.log 31.0 KB errors=26 warnings=12
Log files: FileServer.log 4.0 KB
Log files: Indexer-0.log 8.0 MB errors=2760 warnings=545
Log files: MonitorServer.log 11.0 KB errors=16 warnings=0
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 3.0 KB errors=0 warnings=12
Log files: OMEROweb_brokenrequest.lock 0.0 KB
Log files: OMEROweb_brokenrequest.log 0.0 KB
Log files: PixelData-0.log 4.0 MB errors=1395 warnings=272
Log files: Processor-0.log 496.0 KB errors=160 warnings=24
Log files: Tables-0.log 36.0 KB errors=27 warnings=12
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB errors=0 warnings=6
Log files: master.out 0.0 KB
Log files: nginx_access.log 0.0 KB
Log files: nginx_error.log 0.0 KB
Log files: Total size 18.59 MB

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/Server.app/Contents/ServerRoot/usr/bin:/Applications/Server.app/Contents/ServerRoot/usr/sbin
Environment:PYTHONPATH=/usr/local/opt/omero52/lib/python
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/Volumes/DEC01/OMERO.data' Exists? True Is writable? True
OMERO temp dir:'/Users/markhill/omero/tmp' Exists? True Is writable? True (Size: 12296)

JVM settings: Blitz-${index} -Xmx1932m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx1288m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx1932m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx1288m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 20613)
Django version: 1.8

var/log/master.err:

-! 02/08/17 17:01:24.267 warning: unknown property: `IceSSL.ProtocolVersionMax'

var/log/OMEROweb.log:

2017-02-08 06:18:27,240 WARNI [ py.warnings] (proc.20605) <module>():9 /usr/local/opt/omero52/lib/python/pipeline/utils.py:11: RemovedInDjango19Warning: django.utils.importlib will be removed in Django 1.9.
from django.utils import importlib

The error diagnostic report:

Process: Python [19790]
Path: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.10 (2.7.10)
Code Type: X86-64 (Native)
Parent Process: Python [19552]
Responsible: Python [19790]
User ID: 501

PlugIn Path: /usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/Python
PlugIn Identifier: org.python.python
PlugIn Version: 2.7.13, [c] 2001-2016 Python Software Foundation. (2.7.13)

Date/Time: 2017-02-08 17:02:15.256 +1100
OS Version: Mac OS X 10.12.3 (16D32)
Report Version: 12
Anonymous UUID: 8C420089-D8A6-95BF-2C8F-D50017ED14D4

Time Awake Since Boot: 3700 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Application Specific Information:
crashed on child side of fork pre-exec

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fffe06a9dd6 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fffe0795787 pthread_kill + 90
2 libsystem_c.dylib 0x00007fffe060f4bb __abort + 140
3 libsystem_c.dylib 0x00007fffe060f42f abort + 144
4 org.python.python 0x000000010423f2c6 Py_FatalError + 49
5 org.python.python 0x000000010423e870 PyThreadState_Get + 28
6 org.python.python 0x000000010423b5da Py_InitModule4_64 + 62
7 IcePy.so 0x0000000103b5d94d initIcePy + 45
8 org.python.python 0x00000001029f4190 _PyImport_LoadDynamicModule + 140
9 org.python.python 0x00000001029f2e8c 0x102959000 + 630412
10 org.python.python 0x00000001029f2a60 0x102959000 + 629344
11 org.python.python 0x00000001029f1c38 PyImport_ImportModuleLevel + 1129
12 org.python.python 0x00000001029d7066 0x102959000 + 516198
13 org.python.python 0x000000010296375b PyObject_Call + 99
14 org.python.python 0x00000001029e1e1b PyEval_CallObjectWithKeywords + 165
15 org.python.python 0x00000001029ddc6f PyEval_EvalFrameEx + 8283
16 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
17 org.python.python 0x00000001029db3c7 PyEval_EvalCode + 48
18 org.python.python 0x00000001029f071d PyImport_ExecCodeModuleEx + 241
19 org.python.python 0x00000001029f3427 0x102959000 + 631847
20 org.python.python 0x00000001029f2e8c 0x102959000 + 630412
21 org.python.python 0x00000001029f2aa1 0x102959000 + 629409
22 org.python.python 0x00000001029f1c38 PyImport_ImportModuleLevel + 1129
23 org.python.python 0x00000001029d7066 0x102959000 + 516198
24 org.python.python 0x000000010296375b PyObject_Call + 99
25 org.python.python 0x00000001029e1e1b PyEval_CallObjectWithKeywords + 165
26 org.python.python 0x00000001029ddc6f PyEval_EvalFrameEx + 8283
27 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
28 org.python.python 0x00000001029db3c7 PyEval_EvalCode + 48
29 org.python.python 0x00000001029f071d PyImport_ExecCodeModuleEx + 241
30 org.python.python 0x00000001029f3427 0x102959000 + 631847
31 org.python.python 0x00000001029f36af 0x102959000 + 632495
32 org.python.python 0x00000001029f2e8c 0x102959000 + 630412
33 org.python.python 0x00000001029f2aa1 0x102959000 + 629409
34 org.python.python 0x00000001029f1c38 PyImport_ImportModuleLevel + 1129
35 org.python.python 0x00000001029d7066 0x102959000 + 516198
36 org.python.python 0x000000010296375b PyObject_Call + 99
37 org.python.python 0x00000001029e1e1b PyEval_CallObjectWithKeywords + 165
38 org.python.python 0x00000001029ddc6f PyEval_EvalFrameEx + 8283
39 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
40 org.python.python 0x00000001029db3c7 PyEval_EvalCode + 48
41 org.python.python 0x00000001029f071d PyImport_ExecCodeModuleEx + 241
42 org.python.python 0x00000001029f3427 0x102959000 + 631847
43 org.python.python 0x00000001029f2e8c 0x102959000 + 630412
44 org.python.python 0x00000001029f2a60 0x102959000 + 629344
45 org.python.python 0x00000001029f1c70 PyImport_ImportModuleLevel + 1185
46 org.python.python 0x00000001029d7066 0x102959000 + 516198
47 org.python.python 0x00000001029df534 PyEval_EvalFrameEx + 14624
48 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
49 org.python.python 0x00000001029e2442 0x102959000 + 562242
50 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
51 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
52 org.python.python 0x0000000102981531 0x102959000 + 165169
53 org.python.python 0x000000010296375b PyObject_Call + 99
54 org.python.python 0x000000010296e40c 0x102959000 + 87052
55 org.python.python 0x000000010296375b PyObject_Call + 99
56 org.python.python 0x00000001029aa283 0x102959000 + 332419
57 org.python.python 0x00000001029a5ad8 0x102959000 + 314072
58 org.python.python 0x000000010296375b PyObject_Call + 99
59 org.python.python 0x00000001029de7eb PyEval_EvalFrameEx + 11223
60 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
61 org.python.python 0x00000001029e2442 0x102959000 + 562242
62 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
63 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
64 org.python.python 0x0000000102981531 0x102959000 + 165169
65 org.python.python 0x000000010296375b PyObject_Call + 99
66 org.python.python 0x000000010296e40c 0x102959000 + 87052
67 org.python.python 0x000000010296375b PyObject_Call + 99
68 org.python.python 0x000000010295fe46 PyObject_CallFunctionObjArgs + 190
69 org.python.python 0x00000001029aca27 0x102959000 + 342567
70 org.python.python 0x00000001029a9a2d 0x102959000 + 330285
71 org.python.python 0x00000001029ddb62 PyEval_EvalFrameEx + 8014
72 org.python.python 0x00000001029e24d5 0x102959000 + 562389
73 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
74 org.python.python 0x00000001029e24d5 0x102959000 + 562389
75 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
76 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
77 org.python.python 0x00000001029db3c7 PyEval_EvalCode + 48
78 org.python.python 0x00000001029f071d PyImport_ExecCodeModuleEx + 241
79 org.python.python 0x00000001029f3427 0x102959000 + 631847
80 org.python.python 0x00000001029f2e8c 0x102959000 + 630412
81 org.python.python 0x00000001029f2a60 0x102959000 + 629344
82 org.python.python 0x00000001029f1c70 PyImport_ImportModuleLevel + 1185
83 org.python.python 0x00000001029d7066 0x102959000 + 516198
84 org.python.python 0x00000001029df534 PyEval_EvalFrameEx + 14624
85 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
86 org.python.python 0x00000001029e2442 0x102959000 + 562242
87 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
88 org.python.python 0x00000001029e24d5 0x102959000 + 562389
89 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
90 org.python.python 0x00000001029e24d5 0x102959000 + 562389
91 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
92 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
93 org.python.python 0x00000001029e2442 0x102959000 + 562242
94 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
95 org.python.python 0x00000001029e24d5 0x102959000 + 562389
96 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
97 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
98 org.python.python 0x00000001029e2442 0x102959000 + 562242
99 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
100 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
101 org.python.python 0x00000001029e2442 0x102959000 + 562242
102 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
103 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
104 org.python.python 0x00000001029e2442 0x102959000 + 562242
105 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
106 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
107 org.python.python 0x00000001029e2442 0x102959000 + 562242
108 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
109 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
110 org.python.python 0x00000001029e2442 0x102959000 + 562242
111 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
112 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
113 org.python.python 0x00000001029e2442 0x102959000 + 562242
114 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
115 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
116 org.python.python 0x00000001029e2442 0x102959000 + 562242
117 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
118 org.python.python 0x00000001029e24d5 0x102959000 + 562389
119 org.python.python 0x00000001029deeae PyEval_EvalFrameEx + 12954
120 org.python.python 0x00000001029dba1e PyEval_EvalCodeEx + 1617
121 org.python.python 0x00000001029db3c7 PyEval_EvalCode + 48
122 org.python.python 0x00000001029fb63d 0x102959000 + 665149
123 org.python.python 0x00000001029fb6e0 PyRun_FileExFlags + 133
124 org.python.python 0x00000001029fb231 PyRun_SimpleFileExFlags + 702
125 org.python.python 0x0000000102a0cbca Py_Main + 3094
126 libdyld.dylib 0x00007fffe057b255 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff5d2aae48 rdx: 0x0000000000000000
rdi: 0x0000000000000203 rsi: 0x0000000000000006 rbp: 0x00007fff5d2aae70 rsp: 0x00007fff5d2aae48
r8: 0x0000000000000000 r9: 0x0000000000989680 r10: 0x0000000008000000 r11: 0x0000000000000206
r12: 0x00007fe1ce82b600 r13: 0x0000000103bcfa8a r14: 0x00007fffe93c33c0 r15: 0x0000000102a91478
rip: 0x00007fffe06a9dd6 rfl: 0x0000000000000206 cr2: 0x00000001038ce020

Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133

Binary Images:
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0x102959000 - 0x102a4afff org.python.python (2.7.10 - 2.7.10) <92A4E40A-8B83-3F5F-B5F8-62587FE2EE4C> /System/Library/Frameworks/Python.framework/Versions/2.7/Python
0x102ba2000 - 0x102ba6ff3 _json.so (97) <F30CA32D-6670-3C70-BC9F-5D2265195387> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_json.so
0x102bac000 - 0x102bacfff _bisect.so (97) <DA35D745-0775-3DED-A7D8-78EB6379F15E> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_bisect.so
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0x102c13000 - 0x102c14fff _locale.so (97) <A3C07659-A612-385D-8460-9925FAC7E877> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_locale.so
0x102c99000 - 0x102c9afff _functools.so (97) <C98A98D6-F8AA-31E8-AEBB-1CF609FEA91B> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_functools.so
0x102c9f000 - 0x102ca2fff operator.so (97) <3071A366-6F3E-3139-A22A-ED56C413A982> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/operator.so
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0x102d20000 - 0x102d21ffb time.so (97) <2D302DAB-C9A4-3019-B031-5D9E6FDF9920> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/time.so
0x102d28000 - 0x102d2bffb _struct.so (97) <ABCAF3AD-5239-3E35-852F-98A1A15E3698> /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_struct.so
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0x7fffe063e000 - 0x7fffe0641ffb libsystem_configuration.dylib (888.30.2) <4FE3983C-E4ED-3939-A578-03AD29C99788> /usr/lib/system/libsystem_configuration.dylib
0x7fffe0642000 - 0x7fffe0645fff libsystem_coreservices.dylib (41.4) <1A572B9E-0C47-320F-8C64-7990D0A5FB5A> /usr/lib/system/libsystem_coreservices.dylib
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0x7fffe077c000 - 0x7fffe0785ff3 libsystem_notify.dylib (165.20.1) <E7FD3A7C-DD07-36E2-9FA4-7561F9F114DA> /usr/lib/system/libsystem_notify.dylib
0x7fffe0786000 - 0x7fffe078efe7 libsystem_platform.dylib (126.1.2) <3CA06D4E-C00A-36DE-AA65-3A390097D1F6> /usr/lib/system/libsystem_platform.dylib
0x7fffe078f000 - 0x7fffe0799ff7 libsystem_pthread.dylib (218.30.1) <C869ED7C-BE29-3532-8E69-3A8DA1447EDC> /usr/lib/system/libsystem_pthread.dylib
0x7fffe079a000 - 0x7fffe079dff7 libsystem_sandbox.dylib (592.31.1) <7BBFDF96-293F-3DD9-B3A4-7C168280B441> /usr/lib/system/libsystem_sandbox.dylib
0x7fffe079e000 - 0x7fffe079ffff libsystem_secinit.dylib (24) <5C1F1E47-0F7D-3E25-8DEB-D9DB1F902281> /usr/lib/system/libsystem_secinit.dylib
0x7fffe07a0000 - 0x7fffe07a7fff libsystem_symptoms.dylib (532.30.6) <5D990CF5-B58F-39F7-B375-99B4EC62CFBD> /usr/lib/system/libsystem_symptoms.dylib
0x7fffe07a8000 - 0x7fffe07c8ff7 libsystem_trace.dylib (518.30.7) <6D34D1EA-2A3C-3D2D-803E-A666E6AEEE52> /usr/lib/system/libsystem_trace.dylib
0x7fffe07c9000 - 0x7fffe07ceffb libunwind.dylib (35.3) <9F7C2AD8-A9A7-3DE4-828D-B0F0F166AAA0> /usr/lib/system/libunwind.dylib
0x7fffe07cf000 - 0x7fffe07f8ff7 libxpc.dylib (972.30.7) <65E41BB6-EBD5-3D93-B0BE-B190CEE4DD93> /usr/lib/system/libxpc.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: 3112
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=145.9M resident=0K(0%) swapped_out_or_unallocated=145.9M(100%)
Writable regions: Total=99.0M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=99.0M(100%)

VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Kernel Alloc Once 8K 2
MALLOC 78.2M 17
MALLOC guard page 16K 4
STACK GUARD 56.0M 2
Stack 8192K 2
VM_ALLOCATE 12.3M 19
__DATA 5300K 112
__LINKEDIT 114.3M 43
__TEXT 31.6M 107
__UNICODE 556K 2
shared memory 12K 4
=========== ======= =======
TOTAL 306.1M 303

Model: MacPro6,1, BootROM MP61.0116.B21, 4 processors, Quad-Core Intel Xeon E5, 3.7 GHz, 12 GB, SMC 2.20f18
Graphics: AMD FirePro D300, AMD FirePro D300, PCIe, 2048 MB
Graphics: AMD FirePro D300, AMD FirePro D300, PCIe, 2048 MB
Memory Module: DIMM1, 4 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343531553741465238432D52442020
Memory Module: DIMM2, 4 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343531553741465238432D52442020
Memory Module: DIMM3, 4 GB, DDR3 ECC, 1866 MHz, 0x80AD, 0x484D54343531553741465238432D52442020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x135), Broadcom BCM43xx 1.0 (7.21.171.68.1a5)
Bluetooth: Version 5.0.3f1, 3 services, 27 devices, 1 incoming serial ports
Network Service: Ethernet 2, Ethernet, en1
PCI Card: AMD FirePro D300, Display Controller, Slot-2
PCI Card: AMD FirePro D300, Display Controller, Slot-1
PCI Card: pci17d3,1214, RAID Controller, Thunderbolt@79,0,0
Serial ATA Device: APPLE SSD SM0256F, 251 GB
USB Device: USB 2.0 Bus
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: USB 3.0 Bus
USB Device: Dell QuietKey Keyboard
USB Device: USB Optical Mouse
USB Device: APC AP5631
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Device: ARC5028-T2, Areca, 1, 25.1
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2
Thunderbolt Bus: Mac Pro, Apple Inc., 19.2

Thanks in advance for any help you can provide. Let me know if there is any other information I can provide that may be of assistance.

Posted: **Wed Feb 08, 2017 10:17 am**

Hi Mark,

MarkUNSW wrote:I'm receiving a perplexing python error
Python quit unexpectedly while using the Python plug-in.

Could you perhaps tell us a little more about what steps you've taken up to this point? For example, is Python installed via brew? (from https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/server-install-homebrew.html#requirements)

This sounds as if your installation of Ice wasn't built against the Python installation that's being used like in https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7353#p13092.

Cheers,
~Josh.

Posted: **Thu Feb 09, 2017 7:36 pm**

Yes Python was installed via Homebrew in accordance with the linked instructions.

I was actually receiving that same error you linked in viewtopic.php?f=5&t=7353#p13092 which led me to reinstall ice 3.5 via Homebrew (brew reinstall zeroc-ice35) that appeared to fix the issue and allow me to utilise the omero executable.

Posted: **Thu Feb 09, 2017 8:53 pm**

Mark,

Great, we're glad it worked out! Thank you for letting us know of the good outcome.

Cheers,
Mark

Posted: **Fri Feb 10, 2017 4:34 am**

Apologies as my last post was perhaps less than clear. I am able to utilise the omero executable to perform functions such as <code>omero admin diagnostics</code> and <code>omero admin start</code> however when I execute <code>omero web start</code> I am still receiving the <quote>Python quit unexpectedly while using the Python plug-in.</quote> error.

Thanks,
Mark

Posted: **Fri Feb 10, 2017 11:59 am**

Hi Mark,

sorry to hear you're still having issues. How much do you have installed in this instance of homebrew? Would it be possible to have out the packages which have been installed by the omero formula and start again? It's not clear to us if a sequence of commands might have caused zeroc to be re-installed without the required `--with-python` flag.

If possible, I'd propose removing zeroc and omero, and then retrying the instructions from the website. If you could capture the terminal output, then if you are still having issues after the install we can examine what options are being passed where and try to figure this out.

All the best,
~Josh

Open Microscopy Environment

OMERO 2.7 install - BUILD FAILED

OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED

Re: OMERO 2.7 install - BUILD FAILED