Installation challenges with Mac OSX

jkr · 23 January 2024 20:13

Hi there,
I’ve been working on updating from 2.5.2 to 3.2 and have run into the following issue during installation on Mac OSX despite following all of the instructions. (To make sure this wasn’t as issue with my OSX version, I actually went through an update of OSX to Sonoma 14.3 from a previous version, and still have the same problem.)

When first running " sudo xattr -rd com.apple.quarantine ccpnmr3.2.0" I receive the following errors (which may or may not be associated with my runtime error):
xattr: No such file: ccpnmr3.2.0/miniconda/lib/plugin/libfido2.1.dylib
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/.Python
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/include/python3.4m
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/shutil.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/tempfile.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/lib-dynload
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/encodings
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/_dummy_thread.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/copyreg.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/rlcompleter.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/token.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/base64.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/sre_constants.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/weakref.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/bisect.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/heapq.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/functools.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/hashlib.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/fnmatch.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/warnings.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/codecs.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/_weakrefset.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/io.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/operator.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/os.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/copy.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/genericpath.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/linecache.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/types.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/random.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/keyword.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/reprlib.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/posixpath.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/stat.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/plat-darwin
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/sre_compile.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/locale.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/_collections_abc.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/future.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/config-3.4m
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/hmac.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/tarfile.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/importlib
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/collections
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/ntpath.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/tokenize.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/imp.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/re.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/struct.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/sre_parse.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/abc.py
xattr: No such file: ccpnmr3.2.0/src/python/ccpn/util/nef/venv/lib/python3.4/_bootlocale.py

Then, when I try to run assign (or analysisassign) I receive the following errors and am kicked back to the command line:
rogram licence (non-profit) valid until Mon Jan 4 11:34:08 2100

=================================================================================================================
| AnalysisAssign, version: 3.2.0 |
| |
| Copyright (C) CCPN project (https://www.ccpn.ac.uk) 2014 - 2023 |
| |
| CCPN licence. See Licensing - CCPN - Collaborative Computing Project for NMR. Not to be distributed without prior consent! |
| |
| Active Developers: Ed Brooksbank, Joanna Fox, Victoria A Higman, Luca Mureddu, Eliza Płoskoń, |
| Timothy J Ragan, Brian O Smith, Gary S Thompson & Geerten W Vuister |
| |
| Please cite: Skinner, S.P., Fogh, R.H., Boucher, W., Ragan, T.J., Mureddu, L.G., & Vuister, G.W. |
| CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis |
| J.Biomol.Nmr (2016), 66, 111-124, http://doi.org/10.1007/s10858-016-0060-y |
| |
| DISCLAIMER: This program is offered ‘as-is’. Under no circumstances will the authors, CCPN, |
| the Department of Molecular and Cell Biology, or the University of Leicester be |
| liable of any damage, loss of data, loss of revenue or any other undesired |
| consequences originating from the usage of this software. |

==> Getting user preferences
Error in sys.excepthook:
Traceback (most recent call last):
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/ui/gui/Gui.py”, line 78, in _ccpnExceptionhook
if application and application.hasGui:
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/framework/Framework.py”, line 281, in hasGui
return isinstance(self.ui, Gui)
AttributeError: ‘Assign’ object has no attribute ‘ui’

Original exception was:
Traceback (most recent call last):
File “/Users/xxx/bin/ccpnmr3.2.0/miniconda/lib/python3.10/runpy.py”, line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File “/Users/xxx/bin/ccpnmr3.2.0/miniconda/lib/python3.10/runpy.py”, line 86, in _run_code
exec(code, run_globals)
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/AnalysisAssign/main.py”, line 55, in
main()
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/AnalysisAssign/main.py”, line 45, in main
application = Application(commandLineArguments)
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/framework/Framework.py”, line 198, in init
self.preferences._getUserPreferences()
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/framework/Preferences.py”, line 111, in _getUserPreferences
if (_prefs := self._readPreferencesFile(userPreferencesPath)):
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/framework/Preferences.py”, line 104, in _readPreferencesFile
self._overrideDefaults(_prefs)
File “/Users/xxx/bin/ccpnmr3.2.0/src/python/ccpn/framework/Preferences.py”, line 199, in _overrideDefaults
prefs.appearance.useOnlineDocumentation = False
AttributeError: ‘AttrDict’ object has no attribute ‘appearance’

Hopefully this is something relatively trivial to fix? I cannot find any specific dependencies etc. that I may be missing - I even tried downloading and installing/running version 3.1.1 just to see if this would circumvent the issue and receive exactly the same errors.

Thank you,
Jan Rainey (Dalhousie University, Canada)

VickyH · 24 January 2024 10:14

Hi Jan,

the xattr errors shouldn’t be anything to worry about.
Since the program starts running, it seems as though you’ve successfully got it out of quarantine.

It looks like there might be an error with your Preferences files for some reason. So I would first of all suggest that you remove or rename the .ccpn folder in your home directory (/Users/username). In a terminal the command
ls -a
should list all the directories starting with a . which are otherwise usually hidden.
You will probably have to re-register, but that shouldn’t be a problem.

Let us know how you get on.

Vicky

varioustoxins · 24 January 2024 10:28

Hi Jan

a couple of other questions

which directory is the ccpnmr executable being run from? is the bin directory in your home directory or is it under something like Desktop?
do you have the directory that contains ccpnmr or its parents backed up using iCloud or some other online service?

regards
Gary

jkr · 24 January 2024 11:10

Hi Gary,

In answer to your questions:

This is in the bin directory of my home directory - I could certainly try moving it to another directory if that might be the problem? (I tried a lot of things, but that’s one thing I didn’t try as it hasn’t been an issue with other programs!)
No, I’m not using iCloud or another online backup service for this directory.

Thanks!
Jan

jkr · 24 January 2024 14:06

Dear Vicky,
Thanks very much for your reply! This did indeed fix the problem. Specifically, once I renamed the .ccpn folder in my home directory, I was indeed able to get my current install of version 3.2 running. Once all the updates had been carried out upon startup, I had to re-register (no problem there!) and ver. 3.2 now appears to be fully functional. Looking forward to digging into this!
Thank you for the rapid support and thanks for all your work in developing the software!
Jan

varioustoxins · 26 January 2024 12:47

Dear Jan

Glad to see all is good now. If there is no worries about confidentiality could you send us a copy of your old .ccpn folder and we can try to do some forensics of what was causing the problem…

regards
Gary

jkr · 13 February 2024 18:03

Hi Gary and Vicky - apologies for the delay. I am guessing that this issue is that I had a .ccpn folder from a prior installation of ver. 3.0 in my ~ directory. (I had tried 3.0 back pre-pandemic in 2020, and then reverted to 2.5.2 so had uninstalled/deleted 3.0.) I don’t see a straightforward way to attach a file (or folder) to a post here - happy to send along by email if that would be useful. In terms of a general solution, perhaps just a warning in the installation instructions that if people had a prior version they would need to rename or delete the .ccpn folder in their home directory would be sufficient as a solution here?

Thank you!
Jan

VickyH · 22 February 2024 11:38

Hi Jan,

in theory we’re trying to make sure it’s all back compatible, so people don’t have to do that. But it appears we have missed something. So if you were able to send us your .ccpn folder to support@ccpn.ac.uk, then we could take a look.

Thanks,
Vicky