Hi.
I ran into the deprecation errors as below so was trying to follow this, but I am having the same issue as Tim in that the new yml file doesn't generate those executables (immv, imglob, imcp). The links are there is $FSLDIR/bin but the $FSLDIR/fslpython/envs folder is completely empty except for a .conda_envs_dir_test file which is a blank file.
Any suggestions?
Thanks.
-John
-----Original Message-----
From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of paul mccarthy
Sent: Tuesday, May 7, 2019 8:30 AM
To: [log in to unmask]
Subject: Re: [FSL] Issue with FSL 5.0.11
Hi Tim,
Do imglob, immv, imcp, etc exist in this directory?
$FSLDIR/fslpython/envs/fslpython/bin/
If so, it just means that the symlinks to them weren't created - this may happen if you used "sudo" to run the fslpython_install.sh script, as the final symlink-creation stage may not have been able to find $FSLDIR.
The easiest thing to do at this stage is probably just to manually create them, like so (you may need sudo):
ln -s $FSLDIR/fslpython/envs/fslpython/bin/imcp $FSLDIR/bin/imcp ln -s $FSLDIR/fslpython/envs/fslpython/bin/imglob $FSLDIR/bin/imglob ln -s $FSLDIR/fslpython/envs/fslpython/bin/immv $FSLDIR/bin/immv ln -s $FSLDIR/fslpython/envs/fslpython/bin/atlasq $FSLDIR/bin/atlasq ln -s $FSLDIR/fslpython/envs/fslpython/bin/atlasquery $FSLDIR/bin/atlasquery ln -s $FSLDIR/fslpython/envs/fslpython/bin/fsl_ents $FSLDIR/bin/fsl_ents
Cheers,
Paul
On 03/05/2019, Timothy Hendrickson <[log in to unmask]> wrote:
> Paul,
>
> The versioning errors have disappeared, but it appears that imglob,
> immv, and imcp are not generating. I've attempted to follow the
> instructions
> here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation. but that
> does not make a difference. Could it be due to the yml file?
>
> Best,
>
> -Tim
>
>
> On Thu, Apr 25, 2019 at 4:07 PM paul mccarthy
> <[log in to unmask]>
> wrote:
>
>> 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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