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dcm2niix: 1.0.20200331 -> 1.0.20210317 #103381

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Merged
merged 2 commits into from
May 2, 2021
Merged

dcm2niix: 1.0.20200331 -> 1.0.20210317 #103381

merged 2 commits into from
May 2, 2021
+2 −2

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r-ryantm
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Automatic update generated by nixpkgs-update tools. This update was made based on information from https://github.com/rordenlab/dcm2niix/releases.

meta.description for dcm2niix is: "DICOM to NIfTI converter"

meta.homepage for dcm2niix is: "https://www.nitrc.org/projects/dcm2nii"

meta.changelog for dcm2niix is: ""

Updates performed
  • Version update
To inspect upstream changes
Impact
Checks done (click to expand)
Rebuild report (if merged into master) (click to expand) 
8 total rebuild path(s)

2 package rebuild(s)

2 x86_64-linux rebuild(s)
2 i686-linux rebuild(s)
2 x86_64-darwin rebuild(s)
2 aarch64-linux rebuild(s)


First fifty rebuilds by attrpath
dcm2niix
python37Packages.heudiconv
Instructions to test this update (click to expand)

Either download from Cachix:

nix-store -r /nix/store/dkgscfwf4f6m9mkqq09gr2kh9dgx5zwq-dcm2niix-1.0.20201102 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.

Or, build yourself:

nix-build -A dcm2niix https://github.com/r-ryantm/nixpkgs/archive/806deedb7f574cee62c546f4ac5f32fb1296b293.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:

ls -la /nix/store/dkgscfwf4f6m9mkqq09gr2kh9dgx5zwq-dcm2niix-1.0.20201102
ls -la /nix/store/dkgscfwf4f6m9mkqq09gr2kh9dgx5zwq-dcm2niix-1.0.20201102/bin

Pre-merge build results

We have automatically built all packages that will get rebuilt due to
this change.

This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.

nixpkgs-review encountered an error. Please check the logs at https://r.ryantm.com/log/ for more information.

Maintainer pings

cc @ashgillman for testing.

@ofborg ofborg bot requested a review from ashgillman November 11, 2020 02:24
@SuperSandro2000
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SuperSandro2000 commented Nov 24, 2020 •
edited
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Result of nixpkgs-review pr 103381 run on x86_64-linux 1

1 package failed to build:
  • python37Packages.heudiconv
1 package built:
  • dcm2niix

heudiconv

=================================== FAILURES ===================================
_ test_scans_keys_reproin[--files /build/heudiconv-0.8.0/heudiconv/tests/data] _
heudiconv/tests/test_heuristics.py:106: in test_scans_keys_reproin
    runner(args.split())
heudiconv/cli/run.py:134: in main
    process_args(args)
heudiconv/cli/run.py:352: in process_args
    grouping=args.grouping,)
heudiconv/convert.py:211: in prep_conversion
    dcmconfig=dcmconfig,)
heudiconv/convert.py:303: in convert
    bids_options, tmpdir, dcmconfig)
heudiconv/convert.py:454: in nipype_convert
    eg = convertnode.run()
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py:516: in run
    result = self._run_interface(execute=True)
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py:635: in _run_interface
    return self._run_command(execute)
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py:741: in _run_command
    result = self._interface.run(cwd=outdir)
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/interfaces/base/core.py:419: in run
    runtime = self._run_interface(runtime)
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/interfaces/dcm2nii.py:445: in _run_interface
    runtime, correct_return_codes=(0, 1,)
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/interfaces/base/core.py:814: in _run_interface
    self.raise_exception(runtime)
/nix/store/dhfx9fxgwcqnzy0042sdlyif3qkxvd9v-python3.7-nipype-1.5.1/lib/python3.7/site-packages/nipype/interfaces/base/core.py:745: in raise_exception
    ).format(**runtime.dictcopy())
E   RuntimeError: Command:
E   dcm2niix -b y -z y -x n -t n -m n -f /build/pytest-of-nixbld/pytest-0/test_scans_keys_reproin___file0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff -o . -s n -v n /build/dcm2niixkrh4ydht/convert
E   Standard output:
E
E   Standard error:
E
E   Return code: -11

r-ryantm and others added 2 commits May 2, 2021 03:14
@r-ryantm @lukegb
dcm2niix: 1.0.20200331 -> 1.0.20201102

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@lukegb
dcm2niix: 1.0.20201102 -> 1.0.20210317
884cf29
@lukegb lukegb force-pushed the auto-update/dcm2niix branch from 806deed to 884cf29 Compare May 2, 2021 11:12
@lukegb lukegb changed the title dcm2niix: 1.0.20200331 -> 1.0.20201102 dcm2niix: 1.0.20200331 -> 1.0.20210317 May 2, 2021
@lukegb
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lukegb commented May 2, 2021

@ofborg build python37Packages.heudiconv

@lukegb lukegb merged commit d50819f into NixOS:master May 2, 2021
@r-ryantm r-ryantm deleted the auto-update/dcm2niix branch May 3, 2021 00:02
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