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itk: 5.0.0 -> 5.0.1 #66567

Merged
merged 2 commits into from
Aug 23, 2019
Merged

itk: 5.0.0 -> 5.0.1 #66567

merged 2 commits into from
Aug 23, 2019
+17 −13

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mmahut
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@mmahut mmahut commented Aug 13, 2019 •
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Motivation for this change

Updating to 5.0.1, hopefully fixes a number of builds.

Also moving the source to github.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • 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 nix-review --run "nix-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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cc @viric

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@mmahut
itk: 5.0.0 -> 5.0.1

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3919451 
Changing the source from sourceforge to github.
@mmahut mmahut requested a review from viric August 13, 2019 15:12
@mmahut
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mmahut commented Aug 13, 2019

@GrahamcOfBorg build simpleitk

https://hydra.nixos.org/build/98720007

@mmahut
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mmahut commented Aug 14, 2019

@GrahamcOfBorg build simpleitk

@mmahut
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mmahut commented Aug 14, 2019

The build is too long for ofborg, but I success for me locally. Anyone willing to run nix-review on it, please.

@aanderse
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~/nixpkgs> nix-review pr 66567
...

https://github.com/NixOS/nixpkgs/pull/66567
2 package are marked as broken and were skipped:
c3d seg3d

5 package failed to build:
ants elastix ezminc python27Packages.pyezminc simpleitk

1 package were build:
itk

🤷‍♂️

@mmahut
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mmahut commented Aug 16, 2019

Odd.

@GrahamcOfBorg build simpleitk

@risicle
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risicle commented Aug 17, 2019

Fails on macos 10.13:

builder for '/nix/store/l9g39yk5rmqmpvwrp3pcc0342s8av45g-simpleitk-1.2.2.drv' failed with exit code 2; last 10 log lines:
  [ 97%] Swig source to generate TCL wrapping
  Scanning dependencies of target SimpleITKTclsh
  [ 97%] Building CXX object Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/SimpleITKTCL_wrap.cxx.o
  /tmp/nix-build-simpleitk-1.2.2.drv-0/source/build/Wrapping/Tcl/SimpleITKTCL_wrap.cxx:166:10: fatal error: 'tcl.h' file not found
  #include <tcl.h>
           ^~~~~~~
  1 error generated.
  make[2]: *** [Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/build.make:407: Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/SimpleITKTCL_wrap.cxx.o] Error 1
  make[1]: *** [CMakeFiles/Makefile2:2554: Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/all] Error 2
  make: *** [Makefile:152: all] Error 2

@mmahut
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mmahut commented Aug 17, 2019

ping @bcdarwin do you mind taking a look at ants elastix ezminc python27Packages.pyezminc simpleitk?

@mmahut
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mmahut commented Aug 17, 2019

@risicle do you mind testing again on darwin?

@mmahut
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mmahut commented Aug 17, 2019

@aanderse can you please try again? I get

2 package are marked as broken and were skipped:
c3d seg3d

4 package failed to build:
ants elastix ezminc python27Packages.pyezminc

2 package were build:
itk simpleitk

@risicle
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risicle commented Aug 17, 2019

@risicle do you mind testing again on darwin?

I currently am, but it takes a while...

@aanderse
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@mmahut yes, identical results now:

https://github.com/NixOS/nixpkgs/pull/66567
2 package are marked as broken and were skipped:
c3d seg3d

4 package failed to build:
ants elastix ezminc python27Packages.pyezminc

2 package were build:
itk simpleitk

@mmahut
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mmahut commented Aug 18, 2019

@aanderse do you mind sharing your log? I did the nix-review of this on two separate machines and simpleitk did build for me.

@risicle
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risicle commented Aug 18, 2019

Getting closer on macos now we're including tcl and tk:

  [ 97%] Built target SimpleITKLuaModule_LUA
  [ 97%] Swig source to generate TCL wrapping
  Scanning dependencies of target SimpleITKTclsh
  [ 97%] Building CXX object Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/SimpleITKTCL_wrap.cxx.o
  [ 97%] Linking CXX executable bin/SimpleITKTclsh
  ld: framework not found tcl
  clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
  make[2]: *** [Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/build.make:555: Wrapping/Tcl/bin/SimpleITKTclsh] Error 1
  make[1]: *** [CMakeFiles/Makefile2:2554: Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/all] Error 2
  make: *** [Makefile:152: all] Error 2

I'm trying a rebuild right now with darwin.apple_sdk.frameworks.Tcl included...

@risicle
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risicle commented Aug 18, 2019

Getting closer...

Scanning dependencies of target SimpleITKTclsh
[ 97%] Building CXX object Wrapping/Tcl/CMakeFiles/SimpleITKTclsh.dir/SimpleITKTCL_wrap.cxx.o
[ 97%] Linking CXX executable bin/SimpleITKTclsh
Undefined symbols for architecture x86_64:
  "_Tcl_MainEx", referenced from:
      _main in SimpleITKTCL_wrap.cxx.o
ld: symbol(s) not found for architecture x86_64
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)

@risicle
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risicle commented Aug 18, 2019

Hmm, yes, same error as before. If it builds on hydra, I guess that might be enough - but I suspect there's some impurity at play here.

@mmahut
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mmahut commented Aug 18, 2019

@risicle how do you build it? using nix-review?

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risicle commented Aug 18, 2019

both nix-review and nix-build - same results.

@mmahut
simpleitk: 1.2.0 -> 1.2.2
aa239e9 
Changing the source from sourceforge to github.
@mmahut
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mmahut commented Aug 21, 2019

Odd, I'm going to merge it, as it passes fine on darwin. I have mailed the maintainer for other packages as well, we will mark them as broken if no reply.

@mmahut mmahut merged commit 5fa9205 into NixOS:master Aug 23, 2019
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8.has: clean-up 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10
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