MINC ecosystem #38664

bcdarwin · 2018-04-10T00:34:20Z

Motivation for this change

Adds and updates a large set of tools for working with MINC imaging data in several commits, most but not all logically self-contained. Updates the stale #29782.

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
Built on platform(s)
- NixOS
- macOS
- other Linux distributions
[NA] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[NA] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Fits CONTRIBUTING.md.

…sion)

Mic92 · 2018-04-10T06:55:40Z

@GrahamcOfBorg build ezminc minc_tools mni_autoreg arguments bicpl libminc ants EBTKS c3d elastix perlPackages.TextFormat oobicpl minc_widgets perlPackages.MNI-Perllib itk n3 inormalize

GrahamcOfBorg · 2018-04-10T07:22:54Z

Failure on x86_64-darwin (full log)

Attempted: arguments, ants, c3d, perlPackages.TextFormat, perlPackages.MNI-Perllib, itk

The following builds were skipped because they don't evaluate on x86_64-darwin: ezminc, minc_tools, mni_autoreg, bicpl, libminc, EBTKS, elastix, oobicpl, minc_widgets, n3, inormalize

Partial log (click to expand)

/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsIntermodalityIntrasubject.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsIntroduction.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsJointLabelFusion.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsLongitudinalCorticalThickness.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsMultivariateTemplateConstruction.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsMultivariateTemplateConstruction2.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.ANTSpexec.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsRegistrationSyN.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
/nix/store/dv674n45agkisvr2dczn3d12xr0h6aji-ANTs-2.2.0/bin/.antsRegistrationSyNQuick.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/x030a63qdilnv02pkivfjg44pdxsh5km-bash-4.4-p19/bin/bash"
�[31;1merror:�[0m build of '/nix/store/4z2xjx9wfla3v6pyz46043gfg3ziqjsl-c3d-1.1.0.drv' failed

GrahamcOfBorg · 2018-04-10T07:35:42Z

Failure on x86_64-linux (full log)

Attempted: ezminc, minc_tools, mni_autoreg, arguments, bicpl, libminc, ants, EBTKS, c3d, elastix, perlPackages.TextFormat, oobicpl, minc_widgets, perlPackages.MNI-Perllib, itk, n3, inormalize

Partial log (click to expand)

/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/autocrop: interpreter directive changed from " /usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/make_model: interpreter directive changed from " /bin/sh" to "/nix/store/q1g0rl8zfmz7r371fp5p42p4acmv297d-bash-4.4-p19/bin/sh"
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/mritoself: interpreter directive changed from " /usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/mritotal: interpreter directive changed from " /usr/bin/env perl" to "/nix/store/ggb7k5x9855j10dz99467djx4rplg32b-perl-5.24.3/bin/perl"
checking for references to /tmp/nix-build-mni_autoreg-2017-09-22.drv-0 in /nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22...
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/autocrop
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/mritoself
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/mritotal
/nix/store/f13ljhg32x9zna76pbvniiixpvklh3kh-mni_autoreg-2017-09-22/bin/xfmtool
error: build of ‘/nix/store/h4i19z6bs65dg7y5aqvs5qfiswwgmx3n-elastix-4.8.drv’, ‘/nix/store/kaslwi6v2i2g2wbsqqpf46q33yw7dsx4-c3d-1.1.0.drv’ failed

GrahamcOfBorg · 2018-04-10T07:36:36Z

Failure on aarch64-linux (full log)

Attempted: ezminc, minc_tools, mni_autoreg, arguments, bicpl, libminc, ants, EBTKS, c3d, elastix, perlPackages.TextFormat, oobicpl, minc_widgets, perlPackages.MNI-Perllib, itk, n3, inormalize

Partial log (click to expand)

/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsJointLabelFusion.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsIntroduction.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsIntermodalityIntrasubject.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsCorticalThickness.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsBrainExtraction.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsAtroposN4.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.antsASLProcessing.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
/nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0/bin/.ANTSpexec.sh-wrapped: interpreter directive changed from "/bin/bash" to "/nix/store/3gg2p6n4kv2f0lsxd41f5iz1ivkbzyzr-bash-4.4-p19/bin/bash"
checking for references to /build in /nix/store/qs64w7d22mjkprdl8k8lq89lxrwd6jfz-ANTs-2.2.0...
�[31;1merror:�[0m build of '/nix/store/brzh468q8rdkmr5rg2wz7w67blwmpjha-elastix-4.8.drv', '/nix/store/jhrsdjl8bil6j7p7k5vp2m2lq78r8sz5-c3d-1.1.0.drv' failed

Mic92 · 2018-04-10T07:46:19Z

c3d fails on all targets.

Mic92 · 2018-04-10T07:46:43Z

@GrahamcOfBorg build c3d

GrahamcOfBorg · 2018-04-10T07:48:39Z

Failure on x86_64-darwin (full log)

Attempted: c3d

Partial log (click to expand)

void ImageToImageFilterDefaultCopyInformation(const typename
     ^
2 errors generated.
make[2]: *** [CMakeFiles/cnd_adapters.dir/build.make:639: CMakeFiles/cnd_adapters.dir/adapters/HessianEigenValues.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
8 warnings generated.
make[1]: *** [CMakeFiles/Makefile2:68: CMakeFiles/cnd_adapters.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
builder for '/nix/store/4z2xjx9wfla3v6pyz46043gfg3ziqjsl-c3d-1.1.0.drv' failed with exit code 2
�[31;1merror:�[0m build of '/nix/store/4z2xjx9wfla3v6pyz46043gfg3ziqjsl-c3d-1.1.0.drv' failed

GrahamcOfBorg · 2018-04-10T07:50:10Z

Failure on aarch64-linux (full log)

Attempted: c3d

Partial log (click to expand)

       ~~~~~~~~~~~~~~~~~
       destImage, srcImage);
       ~~~~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/cnd_adapters.dir/build.make:639: CMakeFiles/cnd_adapters.dir/adapters/HessianEigenValues.cxx.o] Error 1
[ 91%] Linking CXX static library libcnd_driver.a
[ 91%] Built target cnd_driver
make[1]: *** [CMakeFiles/Makefile2:695: CMakeFiles/cnd_adapters.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
builder for '/nix/store/jhrsdjl8bil6j7p7k5vp2m2lq78r8sz5-c3d-1.1.0.drv' failed with exit code 2
�[31;1merror:�[0m build of '/nix/store/jhrsdjl8bil6j7p7k5vp2m2lq78r8sz5-c3d-1.1.0.drv' failed

GrahamcOfBorg · 2018-04-10T07:53:08Z

Failure on x86_64-linux (full log)

Attempted: c3d

Partial log (click to expand)

       ComparisonType(),
       ~~~~~~~~~~~~~~~~~
       destImage, srcImage);
       ~~~~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/cnd_adapters.dir/build.make:639: CMakeFiles/cnd_adapters.dir/adapters/HessianEigenValues.cxx.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:695: CMakeFiles/cnd_adapters.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
builder for '/nix/store/7kn7vjn3ngl0isv90s90wj2z4612qcdz-c3d-1.1.0.drv' failed with exit code 2
�[31;1merror:�[0m build of '/nix/store/7kn7vjn3ngl0isv90s90wj2z4612qcdz-c3d-1.1.0.drv' failed

Mic92 · 2018-04-10T07:58:59Z

c3d seems also broken on master : https://hydra.nixos.org/build/72335751/nixlog/2

bcdarwin · 2018-04-10T15:00:27Z

I have tried building c3d from updated sources but the same issue occurs. Perhaps it should be marked broken for now?

Mic92 · 2018-04-10T16:34:05Z

@bcdarwin seems reasonable.

Mic92 · 2018-04-10T16:34:31Z

What is the case regarding elastix?

…c_ecosystem

bcdarwin · 2018-04-10T17:36:36Z

Elastix updated, builds successfully now.

bcdarwin · 2018-04-16T16:30:08Z

@Mic92 -- this pull request is going stale again already; is there anything remaining preventing it from being merged?

bcdarwin · 2018-04-21T21:08:19Z

Thanks!!

bcdarwin and others added 18 commits April 9, 2018 18:05

libminc: 2.3.00 -> 2.3.01 (develop branch)

99dc5f4

perlPackages.TextFormat: init at 0.60

fa2cc0e

minc-tools: 2.3.00 -> 2.3.01 (develop branch)

082b3f1

EBTKS: init at 1.6.50 (develop branch)

e7d447c

perlPackages.MNI-Perllib: init at 0.08

6186489

mni_autoreg: init at 0.99.70

bd460f5

minc-widgets: init at "1.0.0" (package seems to lack a consistent ver…

f532f9f

…sion)

n3: init at 1.0.20

54c543b

inormalize: init at 1.0.20 (develop branch)

e90d1e8

address license/version issues for PR NixOS#29782

cf2aac6

itk: enable more MINC support

c14342d

bicpl: init at 2017-09-10

c9db4ca

ezminc: init at 2017-08-29

de2f369

fix EBTKS version naming

d094f52

arguments: init at 2015-11-30

6972e36

oobicpl: init at 2016-03-02

c148892

disable a second libminc test

524b606

delete broken alias

1595f3c

bcdarwin force-pushed the minc_ecosystem branch from c37fe77 to b31524f Compare April 10, 2018 04:33

metadata fixes: EBTKS, MNI::Perllib, Text::Format

12fa2f9

bcdarwin force-pushed the minc_ecosystem branch from b31524f to 12fa2f9 Compare April 10, 2018 04:54

GrahamcOfBorg added 8.has: clean-up 8.has: package (new) 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 labels Apr 10, 2018

bcdarwin added 2 commits April 10, 2018 13:34

elastix: 4.8 -> 4.9.0

efb02d3

Merge branch 'minc_ecosystem' of github.com:bcdarwin/nixpkgs into min…

1575136

…c_ecosystem

c3d: updated rev still won't compile; mark broken

6908f0c

Mic92 and others added 2 commits April 21, 2018 20:18

Merge branch 'master' into minc_ecosystem

f7785dd

perlPackages.MNI-Perllib: use callPackage instead of import

b1d4962

Mic92 merged commit d6ab165 into NixOS:master Apr 21, 2018

bcdarwin deleted the minc_ecosystem branch April 21, 2018 21:08

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MINC ecosystem #38664

MINC ecosystem #38664

bcdarwin commented Apr 10, 2018

Mic92 commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

Mic92 commented Apr 10, 2018

Mic92 commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

Mic92 commented Apr 10, 2018

bcdarwin commented Apr 10, 2018

Mic92 commented Apr 10, 2018

Mic92 commented Apr 10, 2018

bcdarwin commented Apr 10, 2018 •

edited

bcdarwin commented Apr 16, 2018

bcdarwin commented Apr 21, 2018

MINC ecosystem #38664

MINC ecosystem #38664

Conversation

bcdarwin commented Apr 10, 2018

Motivation for this change

Things done

Mic92 commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

Mic92 commented Apr 10, 2018

Mic92 commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

GrahamcOfBorg commented Apr 10, 2018

Mic92 commented Apr 10, 2018

bcdarwin commented Apr 10, 2018

Mic92 commented Apr 10, 2018

Mic92 commented Apr 10, 2018

bcdarwin commented Apr 10, 2018 • edited

bcdarwin commented Apr 16, 2018

bcdarwin commented Apr 21, 2018

bcdarwin commented Apr 10, 2018 •

edited