Hi Tim,
After further exploration, I've realised that I wasn't quite correct
in my initial diagnosis. But this is due to a change in behaviour
between the different versions of conda, and the
fslpython_environment.yml file that I provided should still work - let
me know if it doesn't.
Cheers,
Paul
On 25/04/2019, Timothy Hendrickson <[log in to unmask]> wrote:
> Ah thank you so much Paul! You have likely saved me many hours of
> troubleshooting.
>
> Best,
>
> -Tim
>
>
> On Thu, Apr 25, 2019 at 3:42 PM paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Tim,
>>
>> I've managed to reproduce this problem - it appears to be due to a
>> change in the way that conda is creating the internal FSL python
>> environment. The version of conda that was available when FSL 5.0.11
>> was released would install all dependencies of our libraries without
>> us having to explicitly list them. However, the latest version of
>> conda only installs the libraries that we list, and does not install
>> any of their dependencies.
>>
>> So your fslpython environment is incomplete. As an interim workaround
>> until we can fix this, after fslinstaller.py has run:
>>
>> 1. Make sure that $FSLDIR is set to the directory that you just
>> installed FSL to
>>
>> 2. take the attached fslpython_environment.yml file and copy it into
>> $FSLDIR/etc/fslconf/ (overriding the file that is already there).
>>
>> 3. Run $FSLDIR/etc/fslconf/fslpython_install.sh
>>
>> Cheers,
>>
>> Paul
>>
>> On 25/04/2019, Timothy Hendrickson <[log in to unmask]> wrote:
>> > Hmm, that does not make a lot of sense. Even though I said that I was
>> > attempting to redownload FSL what I am really doing is using FSL within
>> > a
>> > container so I am not redownloading FSL.
>> >
>> > Has something fundamentally changed about fslinstaller.py within the
>> > last
>> > few weeks that could be resulting in this error?
>> >
>> > Best,
>> >
>> > -Tim
>> >
>> >
>> >
>> > On Tue, Apr 23, 2019 at 4:21 PM paul mccarthy <[log in to unmask]>
>> > wrote:
>> >
>> >> Hi Timothy,
>> >>
>> >> I'm guessing that you overwrote the old FSL installation with the new
>> >> one, and that this has somehow caused the internal fslpython
>> >> environment to become corrupted.
>> >>
>> >> Follow the instructions here to re-install fslpython:
>> >>
>> >>
>> >>
>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation
>> >>
>> >> Cheers,
>> >>
>> >> Paul
>> >>
>> >> On 23/04/2019, Timothy Hendrickson <[log in to unmask]> wrote:
>> >> > Hello,
>> >> >
>> >> > I recently have been using FSL 5.0.11 without issue. I ended up
>> >> > having
>> >> > to
>> >> > redownload FSL and now get the following traceback. Any thoughts?
>> >> >
>> >> > Here is the traceback:
>> >> >
>> >> > Traceback (most recent call last):
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 583, in _build_master
>> >> >
>> >> > ws.require(__requires__)
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 900, in require
>> >> >
>> >> > needed = self.resolve(parse_requirements(requirements))
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 791, in resolve
>> >> >
>> >> > raise VersionConflict(dist, req).with_context(dependent_req)
>> >> >
>> >> > pkg_resources.ContextualVersionConflict: (deprecation 2.0
>> >> > (/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages),
>> >> > Requirement.parse('deprecation<=2.*,>=1.*'), {'fslpy'})
>> >> >
>> >> >
>> >> >
>> >> > During handling of the above exception, another exception occurred:
>> >> >
>> >> > Traceback (most recent call last):
>> >> >
>> >> > File "/usr/local/fsl/bin/imglob", line 6, in <module>
>> >> >
>> >> > from pkg_resources import load_entry_point
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 3241, in <module>
>> >> >
>> >> > @_call_aside
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 3225, in _call_aside
>> >> >
>> >> > f(*args, **kwargs)
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 3254, in _initialize_master_working_set
>> >> >
>> >> > working_set = WorkingSet._build_master()
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 585, in _build_master
>> >> >
>> >> > return cls._build_from_requirements(__requires__)
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 598, in _build_from_requirements
>> >> >
>> >> > dists = ws.resolve(reqs, Environment())
>> >> >
>> >> > File
>> >> >
>> >>
>> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
>> >> > line 786, in resolve
>> >> >
>> >> > raise DistributionNotFound(req, requirers)
>> >> >
>> >> > pkg_resources.DistributionNotFound: The 'deprecation<=2.*,>=1.*'
>> >> > distribution was not found and is required by fslpy
>> >> >
>> >> > Best,
>> >> >
>> >> > -Tim
>> >> >
>> >> >
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