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libminc: 2.4.03 -> unstable-2020-07-17 #93675

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merged 12 commits into from Oct 7, 2020
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@bcdarwin bcdarwin commented Jul 22, 2020

and update reverse dependencies accordingly

Motivation for this change
  • update libminc; most importantly a fix for a scaling bug (BIC-MNI/libminc#109)
  • libminc builds against default hdf5, so drop hdf5_1_8 from tree
  • the location of CMake files has changed, so the builds of its reverse dependencies need to be updated
Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
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@bcdarwin bcdarwin commented Jul 30, 2020

Getting some weird resource temporarily unavailable test failures on nix.ci but nixpkgs-review pr succeeds locally; probably some OfBorg resource limit?

36/50 Test #45: minc2-slice-test .................***Failed    0.02 sec
/build/source/libsrc/netcdf_convenience.c:573 (from miopen): Unable to open file '/build/source/build/testdir/3D_minc2_int.mnc'
/build/source/build/testdir/3D_minc2_int.mnc: Resource temporarily unavailable
/build/source/libsrc2/volume.c:1390 (from miopen): Unable to open file '/build/source/build/testdir/3D_minc2_int.mnc'
can't open /build/source/build/testdir/3D_minc2_int.mnc, error -1
@bcdarwin bcdarwin force-pushed the bcdarwin:update-libminc branch from ad2d095 to ae7b398 Aug 16, 2020
@bcdarwin bcdarwin force-pushed the bcdarwin:update-libminc branch 2 times, most recently from 150181d to b99b4c2 Sep 22, 2020
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@bcdarwin bcdarwin commented Sep 22, 2020

Rebased onto master and resolved breakage from another PR (#91071).

@bcdarwin bcdarwin requested a review from lheckemann Sep 22, 2020
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@lheckemann lheckemann left a comment

Wow, upstream could do with some more releases :D

That aside, LGTM.

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@lheckemann lheckemann commented Sep 23, 2020

That is indeed an, uh, interesting failure on ofborg. Let's just kick it.

@ofborg build EBTKS bicgl bicpl conglomerate inormalize minc_tools mni_autoreg n3 oobicpl

@bcdarwin bcdarwin force-pushed the bcdarwin:update-libminc branch from b99b4c2 to cbecc75 Sep 23, 2020
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@bcdarwin bcdarwin commented Sep 23, 2020

libminc tests are still weirdly failing, so I've disabled parallel building -- perhaps that will help.

@bcdarwin bcdarwin force-pushed the bcdarwin:update-libminc branch from cbecc75 to 7aa0753 Oct 5, 2020
@bcdarwin bcdarwin force-pushed the bcdarwin:update-libminc branch from 7aa0753 to 95439a7 Oct 6, 2020
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@bcdarwin bcdarwin commented Oct 6, 2020

@lheckemann turns out the tests can't be run in parallel (and enableParallelBuilding doesn't control ctest); see BIC-MNI/libminc#110. Anyway, good to go now.

@bcdarwin bcdarwin requested a review from lheckemann Oct 6, 2020
@lheckemann lheckemann merged commit a25bd66 into NixOS:master Oct 7, 2020
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tests tests
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EBTKS, EBTKS.passthru.tests, bicgl, bicgl.passthru.tests, bicpl, bicpl.passthru.tests, conglomerate, conglomerate.passthru.tests, inormalize, inormalize.passthru.tests, libminc, libminc.passthru.tests, minc_tools, minc_tools.passthru.tests, mni_autoreg, mni_autoreg.passthru.tests, n3, n3.passthru.tests, oobicpl, oobicpl.passthru.tests on aarch64-linux Success
Details
EBTKS, EBTKS.passthru.tests, bicgl, bicgl.passthru.tests, bicpl, bicpl.passthru.tests, conglomerate, conglomerate.passthru.tests, inormalize, inormalize.passthru.tests, libminc, libminc.passthru.tests, minc_tools, minc_tools.passthru.tests, mni_autoreg, mni_autoreg.passthru.tests, n3, n3.passthru.tests, oobicpl, oobicpl.passthru.tests on x86_64-linux Success
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Evaluation Performance Report Evaluator Performance Report
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Wait for ofborg
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grahamcofborg-eval ^.^!
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grahamcofborg-eval-check-maintainers matching changed paths to changed attrs...
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grahamcofborg-eval-check-meta config.nix: checkMeta = true
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grahamcofborg-eval-darwin nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./pkgs/t
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grahamcofborg-eval-lib-tests nix-build --arg pkgs import ./. {} ./lib/tests/release.nix
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grahamcofborg-eval-nixos nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./nixos/
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grahamcofborg-eval-nixos-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./nixos/
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grahamcofborg-eval-nixos-options nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./nixos/
Details
grahamcofborg-eval-nixpkgs-manual nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./pkgs/t
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grahamcofborg-eval-nixpkgs-tarball nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./pkgs/t
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grahamcofborg-eval-nixpkgs-unstable-jobset nix-instantiate --arg nixpkgs { outPath=./.; revCount=999999; shortRev="95439a7"; rev="95439a7e7d711c172c9b5160488f055f3d82d07a"; } ./pkgs/t
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grahamcofborg-eval-package-list nix-env -qa --json --file .
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grahamcofborg-eval-package-list-no-aliases nix-env -qa --json --file . --arg config { allowAliases = false; }
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@bcdarwin bcdarwin deleted the bcdarwin:update-libminc branch Oct 7, 2020
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