nipy / heudiconv

Flexible DICOM conversion into structured directory layouts
https://heudiconv.readthedocs.io
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Conda installation problem #705

Closed papaya454 closed 11 months ago

papaya454 commented 12 months ago

Summary

trying to install HeuDiConv through pip and conda. pip was installed correctly but it was not showing any kind of series information when trying to convert, so I have reverted to downloading HeuDiConv through conda. However, the terminal just keeps running with debugging and solving environment sequence for hours. I will have to terminate session on my end.

terminal spits out something like this

Collecting package metadata (current_repodata.json): \ DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
| DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
/ DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/current_repodata.json HTTP/1.1" 304 0
- DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/osx-64/current_repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/osx-64/current_repodata.json HTTP/1.1" 304 0
\ WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1
done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): \ DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): repo.anaconda.com:443
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/osx-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/osx-64/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/r/noarch/repodata.json HTTP/1.1" 304 0
DEBUG:urllib3.connectionpool:https://repo.anaconda.com:443 "GET /pkgs/main/noarch/repodata.json HTTP/1.1" 304 0
\ WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0.*, but conda is ignoring the .* and treating it as 1.6.0
done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

I noticed there were some issues in the past about conda installation but was unsure if that was resolved at all. Any help would be much appreciated. Thank you!

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yarikoptic commented 11 months ago

(un)fortunately it might be nothing we can solve in heudiconv or to be more precise in https://github.com/conda-forge/heudiconv-feedstock recipe for conda-forge. Check conda info -- which architecture the laptop is? if M1/arm -- then see https://github.com/conda-forge/nipype-feedstock/issues/99 which I just filed. If still regular x86_64 - we will dig more, but file an issue against https://github.com/conda-forge/heudiconv-feedstock/ . Meanwhile I did conda create -n heudiconv-test -y -c conda-forge heudiconv on Linux conda installation -- seems to installed just fine.

yarikoptic commented 11 months ago

ok, if it was M1 OSX, problem is now resolved since there is now build of nipype for arm in conda-forge but it would work only for python < 3.11. I just did

datalad@26696 ~ % conda create -n heudiconv -c conda-forge -y heudiconv

and it quickly created environment with

(heudiconv) datalad@26696 ~ % python --version
Python 3.10.12
(heudiconv) datalad@26696 ~ % heudiconv --version
1.0.0