Building ITK on Windows

[muschellij2]

Building ITK on Windows (through R)

I'm trying to build ITK on Windows, through R in the ITKR package (https://github.com/muschellij2/ITKR). I'm testing this through appveyor (https://ci.appveyor.com/project/muschellij2/itkr). I'm getting the following error:

[ 73%] Building C object Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/H5Defl.c.obj
In file included from C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5private.h:615:0,
                 from C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5Defl.c:29:
C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5Defl.c: In function 'H5D__efl_read':
C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5win32defs.h:57:66: error: expected expression before ')' token
 #define HDopen(S,F,...)       _open(S, F | _O_BINARY, __VA_ARGS__)
                                                                  ^
C:\run\ITKR.Rcheck\00_pkg_src\ITKR\src\itks\Modules\ThirdParty\HDF5\src\itkhdf5\src\H5Defl.c:291:18: note: in expansion of macro 'HDopen'
         if((fd = HDopen(full_name, O_RDONLY)) < 0)
                  ^
Modules\ThirdParty\HDF5\src\itkhdf5\src\CMakeFiles\hdf5-static.dir\build.make:770: recipe for target 'Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/hdf5-static.dir/H5Defl.c.obj' failed

This worked using commit 4f89edd, but not the latest or anything with respect to v5.0.

Steps to Reproduce

The steps can be seen here: https://ci.appveyor.com/project/muschellij2/itkr

1. The main configure script is https://github.com/muschellij2/ITKR/blob/master/configure.win
2. The make version is mingw32-make, and the Makevars necessary to reproduce are: https://github.com/muschellij2/ITKR/blob/master/src/Makevars.win
3. See the attached 00install.txt file below.

Expected behavior

Successful build such as https://ci.appveyor.com/project/muschellij2/itkr/build/1.0.278

Actual behavior

Build failure such as https://ci.appveyor.com/project/muschellij2/itkr/build/1.0.282

Reproducibility

100% of the builds with

Versions

ITK_VERSION_MAJOR = 5
ITK_VERSION_MINOR = 0
ITK_VERSION_PATCH = 0

Environment

Windows on Appveyor (I believe Windows Server 2012 R2 )

Additional Information

I've uploaded the CMakeLists and the installation output
CMakeLists.txt
00install.txt

[thewtex]

Hi @muschellij2, when I try building with the MinGW Makefiles CMake generator, I get an error that sh.exe cannot be in the PATH -- it looks like sh.exe might be in the PATH in this case?

Could you please try downloading ninja.exe, use the Ninja generator, and see what happens?

From this note, it sounds like Visual Studio is being falsely detected or other setup is not correct:

ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5win32defs.h

Lines 50 to 57 in 13bbb31

	/* _O_BINARY must be set in Windows to avoid CR-LF <-> LF EOL
	* transformations when performing I/O. Note that this will
	* produce Unix-style text files, though.
	*
	* Also note that the variadic macro is using a VC++ extension
	* where the comma is dropped if nothing is passed to the ellipsis.
	*/
	#define HDopen(S,F,...) _open(S, F | _O_BINARY, __VA_ARGS__)

[muschellij2]

I have been able to build before with MinGW. I need to use MinGW vs. ninja as this is the recommended and default way when building with R packages.

In https://github.com/muschellij2/ITKR/blob/master/configure.win#L58, The CMAKE_SH will remove the sh.exe error.

    -DCMAKE_SH:BOOL=OFF 

If you take sh.exe out of the PATH, then R will not be able to run anything. Also the configure.win needs git in the path, which also may have an sh.exe in PATH (but I believe it was the Rtools sh.exe if I remember correctly).

I need to check with @appveyor as it seems as though the configuration may have changed. I think the .Rproj file that's confusing appveyor: https://www.appveyor.com/docs/build-phase/. I'll try to remove and rerun.

[muschellij2]

Deleted the Rproj file in commit muschellij2/ITKR@9ca09e1, but it still fails with the same error: https://ci.appveyor.com/project/muschellij2/itkr/build/job/1vngo4na0eryy4h0

As per https://help.appveyor.com/discussions/problems/12705-custom-build-script-script-mode, I'm going to try to add

build: off

muschellij2/ITKR@7d08051
to try to ensure build is off and Visual Studio isn't being detected

[muschellij2]

Still a fail with these modifications: https://ci.appveyor.com/project/muschellij2/itkr/build/1.0.289/job/vg0toj68d27fgams

[thewtex]

@muschellij2 I confirmed the build error locally with both mingw32-make and ninja.

I created a patch here:

http://review.source.kitware.com/#/c/23773/

I will submit this to upstream HDF5.

However, there were a lot of failing tests, which I think are unrelated.

So, I would recommend trying the tip of the release-4.13 branch.

[muschellij2]

Thanks for the update! Looks like it will fix the build. I will pull in when it's in the upstream branch (as I need v5 for ANTs building), but I appreciate the fix. @adigherman @stnava - this should help with Windows builds

[muschellij2]

Has this been incorporated? I don't see in the source.

[thewtex]

http://review.source.kitware.com/#/c/23773/

This caused issues with Visual Studio, so it was not incorporated.

We have been working with the HDF5 folks, who are in the process of opening up their issue tracker and source repository.

HDF5 1.10.4 came out recently -- I am working on updating our sources. Your help testing would be appreciated.

[thewtex]

@muschellij2 does this branch fix the build issue?

#397