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mfitzp / pathomx

Workflow based scientific analysis built on Python
https://www.mfitzp.com/tools/pathomx/
GNU General Public License v3.0
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Mac OSX installation trouble #19

Open KWhitesonLab opened 10 years ago

KWhitesonLab commented 10 years ago

Hi, I am a new potential user of Pathomx but I was not able to install it on my mac. I'm running OSX 10.7.5 - I realize that might be the problem right there, updating to 10.9 could solve the problem. Nevertheless, FYI, when I click on the dmg, drag the unpacked Pathomx to my Applications folder and try to open it, this immediately appears in the crash report (see below).

Any advice is appreciated! Katrine http://www.whiteson.org/katrine/

Process: launchd [1167] Path: /Applications/Pathomx.app/Contents/MacOS/Pathomx Identifier: launchd Version: ??? (???) Code Type: X86-64 (Native) Parent Process: launchd [222]

Date/Time: 2014-04-15 13:42:22.405 -0700 OS Version: Mac OS X 10.7.5 (11G63b) Report Version: 9

Crashed Thread: Unknown

Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00007fff5fc01028

Backtrace not available

Unknown thread crashed with X86 Thread State (64-bit): rax: 0x0000000000000055 rbx: 0x0000000000000000 rcx: 0x0000000000000000 rdx: 0x0000000000000000 rdi: 0x0000000000000000 rsi: 0x0000000000000000 rbp: 0x0000000000000000 rsp: 0x0000000000000000 r8: 0x0000000000000000 r9: 0x0000000000000000 r10: 0x0000000000000000 r11: 0x0000000000000000 r12: 0x0000000000000000 r13: 0x0000000000000000 r14: 0x0000000000000000 r15: 0x0000000000000000 rip: 0x00007fff5fc01028 rfl: 0x0000000000010203 cr2: 0x00007fff5fc01028 Logical CPU: 0

Binary images description not available

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: 1966 thread_create: 1 thread_set_state: 0

Model: MacBookPro8,1, BootROM MBP81.0047.B26, 2 processors, Intel Core i7, 2.8 GHz, 8 GB, SMC 1.68f98 ...

mfitzp commented 10 years ago

Hi Katrine, thanks for your bug report, much appreciated. I've had a similar report from someone running 10.6.8 and would like to fix this without forcing upgrades.

From reading up on it I think I need to build a separate version for each major release of MacOS X. Unfortunately I don't have access to anything but Mountain Lion at the moment, but I'm looking to see if there is a way to build backwards-compatible releases on it.

Will update this once I figure something out!

NiGem commented 10 years ago

1 like to commend you on the work u have done mfitzp :) Brilliant 2 We have tried both running the latest one 2.5 on 10.8.5 and building it from scratch (using homebrew recipie) but start up stalls for us too in both cases. which indeed makes us wonder if thereare other tweaks or dependencies for mac os x ?

Do u use 10,9 or 10.8 for compiling make?

mfitzp commented 10 years ago

Thanks @NiGem! Unfortunately yes I'm building on 10.9. Thanks for trying to build from scratch using homebrew. Have you attempted to run Pathomx from the command line with:

python Pathomx.py

If you can try that and let me know any output you get. It may be that I need to tweak the install instructions a bit, but it should be possible to get it to run (and then build) on 10.8 - there is nothing 10.9 specific about the code.

KWhitesonLab commented 10 years ago

Hi guys, I have gotten the same errors trying to install on 10.9 actually. The command line is a good idea.

;) Katrine

On May 22, 2014, at 11:59 AM, Martin Fitzpatrick notifications@github.com wrote:

Thanks @NiGem! Unfortunately yes I'm building on 10.9. Thanks for trying to build from scratch using homebrew. Have you attempted to run Pathomx from the command line with:

python Pathomx.py If you can try that and let me know any output you get. It may be that I need to tweak the install instructions a bit, but it should be possible to get it to run (and then build) on 10.8 - there is nothing 10.9 specific about the code.

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NiGem commented 10 years ago

DEBUG:root:Loading qt.py Traceback (most recent call last): File "/Applications/Canopy.app/appdata/canopy-1.3.0.1715.macosx-x86_64/Canopy.app/Contents/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/Applications/Canopy.app/appdata/canopy-1.3.0.1715.macosx-x86_64/Canopy.app/Contents/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/Users/Shared/pathomx/pathomx/Pathomx.py", line 29, in from .qt import File "pathomx/qt.py", line 9, in from PyQt5.QtGui import ImportError: No module named PyQt5.QtGui

I believe it is an issue on PyQt5 and Python 3

By default do you only use the Celler folder of homebrew ?

NiGem commented 10 years ago

perhaps this may be doing it ?

This formula is keg-only, so it was not symlinked into /usr/local.

Qt 5 conflicts Qt 4 (which is currently much more widely used).

Generally there are no consequences of this for you. If you build your own software and it requires this formula, you'll need to add to your build variables:

LDFLAGS:  -L/usr/local/opt/qt5/lib
CPPFLAGS: -I/usr/local/opt/qt5/include
mfitzp commented 10 years ago

Ah! On Mac I have only successfully run Pathomx using Python2.7. It should (technically) run with Python3.4+ too - as it does on Linux - but it is untested.

It looks from the error output that it's simply not finding PyQt5. Is PyQt5 installed? Note that you also need to install PyQt5 as well as Qt5!

If it is, is it installed under Python3 or Python2.7? Are you running Pathomx.py with python or python3? It shouldn't matter which but you must run it from the version with PyQt5 installed.

You can give this a test by starting a python shell with either python or python3 then trying to do import PyQt5 and from PyQt5 import QtGui If Qt5 isn't linked you could try brew link qt5.

Unsure about the LDFLAGS and CPPFLAGS but I don't have them set on my system.

KWhitesonLab commented 10 years ago

Wow, thank you for looking into this! I am out of town, back at work Tuesday, ill let you know how it goes...

;) K

On May 23, 2014, at 6:22 AM, Martin Fitzpatrick notifications@github.com wrote:

Ah! On Mac I have only successfully run Pathomx using Python2.7. It should (technically) run with Python3.4+ too - as it does on Linux - but it is untested.

It looks from the error output that it's simply not finding PyQt5. Is PyQt5 installed? Note that you also need to install PyQt5 as well as Qt5!

If it is, is it installed under Python3 or Python2.7? Are you running Pathomx.py with python or python3? It shouldn't matter which but you must run it from the version with PyQt5 installed.

You can give this a test by starting a python shell with either python or python3 then trying to do import PyQt5 and from PyQt5 import QtGui If Qt5 isn't linked you could try brew link qt5.

Unsure about the LDFLAGS and CPPFLAGS but I don't have them set on my system.

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NiGem commented 9 years ago

It works :)

mfitzp commented 9 years ago

@Katreenuh Can you confirm whether you ever managed to get it working on 10.7?

KWhitesonLab commented 9 years ago

I haven't tried recently, I will and I'll let you know.

Thanks! Katrine

On Nov 30, 2014, at 1:54 PM, Martin Fitzpatrick notifications@github.com wrote:

@Katreenuh Can you confirm whether you ever managed to get it working on 10.7?

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