Package Details: mygnuhealth 1.0.4-1

Git Clone URL: https://aur.archlinux.org/mygnuhealth.git (read-only, click to copy)
Package Base: mygnuhealth
Description: The GNU Health Personal Health Record (PHR)
Upstream URL: https://www.gnuhealth.org
Keywords: bioinformatics GNUHealth healthcare mHealth PHR PIM
Licenses: GPL3
Submitter: meanmicio
Maintainer: meanmicio (z3ntu)
Last Packager: meanmicio
Votes: 3
Popularity: 0.61
First Submitted: 2021-07-08 20:52
Last Updated: 2021-08-22 21:13

Latest Comments

meanmicio commented on 2021-07-10 12:39

Thanks for reporting!

Hmm. Can not reproduce it... It's strange, because numpy core.multiarray is part of the main package (python-numpy) and is required by python-matplotlib.

Can you please provide the full trace of the error?

Also, could you provide this info, from the Python interpreter:

Python 3.9.6 (default, Jun 30 2021, 10:22:16) [GCC 11.1.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import numpy.core.multiarray print (numpy.core.multiarray) <module 'numpy.core.multiarray' from '/usr/lib/python3.9/site-packages/numpy/core/multiarray.py'> print (numpy.version) 1.20.3

alerque commented on 2021-07-10 09:25

I think you're missing a dependency on numpy:

ImportError: numpy.core.multiarray failed to import

meanmicio commented on 2021-07-09 12:45

Fixed file mode, and cleaned up PKGBUILD. It should work now :) (https://paste.rs/qul)

meanmicio commented on 2021-07-09 12:07

True. I have made a more specific workaround, that changes the permission only on the specific variants.db file

https://pastebin.com/C6E3tgjS

Probably would fit better at the end of the build() function, but it does seem to work on package(), as long as it runs before the actual setup install.

If it sounds good to you, then we'll increment pkgrel :)

alerque commented on 2021-07-09 10:22

That sounds about right. This commit message and diff is probably a more aggressive fix than we want, but along the right lines of fixing the files in $pkgdir after installing stuff there in package().

meanmicio commented on 2021-07-09 09:30

I think we're hitting this issue https://github.com/pypa/setuptools/issues/1328#issuecomment-718556363

When installing the application with pip, it does set the right permissions on "/usr/lib/python3.9/site-packages/mygnuhealth/data/variants.db".

alerque commented on 2021-07-09 08:46

You can fix in in package() after Python does it's thing, but that actually sounds like an upstream bug. It should be reported ... somewhere.

meanmicio commented on 2021-07-09 08:17

Good morning, alerque!

Thank you for reporting! It's a filemode issue:

/usr/lib/python3.9/site-packages/mygnuhealth/data/variants.db

Currently is only for rw for root.

The file /usr/lib/python3.9/site-packages/mygnuhealth/data/variants.db Must be read-only but for all users (mod 444). I will check on how to give the proper 444 on that file in PKGBUILD.

Best

alerque commented on 2021-07-09 07:12

I think this is still missing something, I'm not sure whether this is a missing dep or an upstream bug or what. I installed it myself and got this:

$ mygnuhealth
Initializing MyGNUHealth version 1.0.1
Directory exists... skipping
Found myGNUHealth configuration file.. skipping
Verifying MyGNUHealth Database.....
DB file not found.
Traceback (most recent call last):
  File "/usr/bin/mygnuhealth", line 32, in <module>
    main()
  File "/usr/lib/python3.9/site-packages/mygnuhealth/mygh.py", line 50, in main
    from mygnuhealth.profile_settings import ProfileSettings
  File "/usr/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/__feature__.py", line 142, in _import
    return original_import(name, *args, **kwargs)
  File "/usr/lib/python3.9/site-packages/mygnuhealth/profile_settings.py", line 12, in <module>
    from mygnuhealth.core import (get_personal_key, get_user_profile,
  File "/usr/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/__feature__.py", line 142, in _import
    return original_import(name, *args, **kwargs)
  File "/usr/lib/python3.9/site-packages/mygnuhealth/core.py", line 41, in <module>
    vardb = TinyDB(varfile, access_mode='r')
  File "/usr/lib/python3.9/site-packages/tinydb/database.py", line 94, in __init__
    self._storage = storage(*args, **kwargs)  # type: Storage
  File "/usr/lib/python3.9/site-packages/tinydb/storages.py", line 105, in __init__
    self._handle = open(path, mode=self._mode, encoding=encoding)
PermissionError: [Errno 13] Permission denied: '/usr/lib/python3.9/site-packages/mygnuhealth/data/variants.db'