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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
Merged

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

merged 12 commits into from Oct 7, 2020

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bcdarwin
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@bcdarwin bcdarwin commented Jul 22, 2020 •
edited

and update reverse dependencies accordingly

Motivation for this change
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 commented Jul 30, 2020 •
edited

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 update-libminc branch 2 times, most recently from 150181d to b99b4c2 Compare September 22, 2020 20:59
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Rebased onto master and resolved breakage from another PR (#91071).

lheckemann
lheckemann approved these changes Sep 23, 2020
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Wow, upstream could do with some more releases :D

That aside, LGTM.

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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

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

@bcdarwin
libminc: 2.4.03 -> unstable-2020-07-17
3862e92 
- propagate hdf5 and netcdf since essentially every reverse dep of libminc depends on these
- switch to default HDF5 from 1.8.x series
- one resolved test failure and one new error (less concerning than before)
@bcdarwin
minc_tools: unstable-2019-12-04 -> unstable-2020-07-25
91a429a
@bcdarwin
EBTKS: update LIBMINC_DIR due to libminc update
da69e47
@bcdarwin
bicpl: fix LIBMINC_DIR due to libminc CMake changes
2c33e9d
@bcdarwin
inormalize: update LIBMINC_DIR and dependencies due to libminc update
7772e24
@bcdarwin
n3: 2017-09-18 -> 2018-08-09
9a19078 
- update LIBMINC_DIR and EBTKS_DIR due to CMake updates in those packages
@bcdarwin
mni_autoreg: update LIBMINC_DIR due to CMake changes in libminc
83d0571
@bcdarwin
oobicpl: update LIBMINC_DIR due to libminc CMake changes
8594691
@bcdarwin
EZminc: update LIBMINC_DIR to reflect libminc CMake changes
44f2bf8
@bcdarwin
conglomerate: update LIBMINC_DIR to reflect libminc CMake changes
e673c28
@bcdarwin
bicgl: update LIBMINC_DIR due to libminc CMake changes
44d854a
@bcdarwin
hdf5_1_8: remove
95439a7 
- no longer needed as `libminc` has been updated to use the default hdf5
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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.

@lheckemann lheckemann merged commit a25bd66 into NixOS:master Oct 7, 2020
@bcdarwin bcdarwin deleted the update-libminc branch October 7, 2020 17:04
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