[Rd] Seeking advice regarding compilation of large libraries using RTools (Windows)

Richard Beare richard.beare at gmail.com
Wed Mar 8 01:09:56 CET 2017

So far I've been using the separate cmake package (direct from kitware),
rather than one available via msys2 (as I started without msys2). I'll have
a play with the msys2 versions.

The problem definitely seems to be with ld - it sits at high load for days
at a time, and I haven't seen it complete successfully on the test exe
files. They also hang around when I kill the make.

I'm having a play with building libraries but not test infrastructure,
although this isn't a long term solution.

Sounds like clang is something worth checking out - any comments on whether
it is close to working with R?

On Wed, Mar 8, 2017 at 10:35 AM, Ray Donnelly <rdonnelly at continuum.io>

> On Mon, Mar 6, 2017 at 8:21 PM, Richard Beare <richard.beare at gmail.com>
> wrote:
>> Yep - simpleITK is available at github.com/SimpleITK/SimpleITK. There's
>> also github.com/SimpleITK/SimpleITKRInstaller - a devtools based
>> installer
>> for mac and linux.
>> CMake has a range of build environments. I experimented with MSYS2 and
>> mingw makefiles, but had trouble with incompatibilities in the path
>> required by CMake and those options - from memory the sh in RTools/bin
>> caused problems. Although it sounds like you are saying it is necessary to
>> install the MSYS2 system as well.
> MSYS2 has two variants (3 distinctly named packages) of CMake:
> mingw-w64-{i686,x86_64}-cmake and cmake. Which of these (if any) did you
> use? I cannot state without experimenting which should be used, but the
> mingw-w64 prefixed ones are usually the ones you want to generate native
> code.
>> The unix makefile option for CMake appears to work well until the linking
>> stage. Ninja has problems at a similar stage.
>> I'll steer clear of dll's, as you suggest. I'm checking those links for
>> compiler/links flags to see if we're missing anything
> I would be happy to see if I can get it to compile in the Anaconda
> Distribution too. Here we prefer DLLs. The gnu ld linker on Windows is very
> slow and doesn't seem to scale too well. I do not expect cross-compiling
> would make it much faster. The clang linker (ldd) is nearly viable on
> Windows and apparently much faster. I'm not sure if this near-viability is
> in relation to using it in msvc mode, gcc mode or both (or even whether it
> implements frontends for both).
>> Thanks
>> On Mon, Mar 6, 2017 at 9:51 PM, Jeroen Ooms <jeroenooms at gmail.com> wrote:
>> > On Mon, Mar 6, 2017 at 6:33 AM, Richard Beare <richard.beare at gmail.com>
>> > wrote:
>> > > I am working on the SimpleITK package for R. This is an enormous
>> package
>> > > that is largely automatically generated via a set of swig/json/lua
>> magic,
>> > > and is working well under linux and osx.
>> >
>> > Is it available somewhere so we can try it?
>> >
>> >
>> > > However we're having a lot of trouble with the Windows side. In fact,
>> we
>> > are struggling to get the base libraries to build using the RTools 3.4
>> > toolchain, even before the worrying about the R-specific parts.
>> >
>> > What build environment do you use? The version of gcc with Rtools
>> > should be ok, but the Rtools build utilities in the "bin" folder (in
>> > particular 'make') are old and a frequent source of problems. However
>> > for building external libs you can use other tools, for example those
>> > from msys2. Just make sure you use gcc/g++ from Rtools.
> >
>> >
>> > > The current issue is very long time (possibly infinite) linking of
>> dlls,
>> > or
>> > > test executables. I've tried using a FAT32 file system for the build,
>> as
>> > > suggested by some old bug reports, but still have the issue.
>> >
>> > On Windows you can avoid the run-time dll mess by building static libs
>> > of external libraries. See rwinlib for examples:
>> > https://github.com/rwinlib
>> >
>> >
>> > > Any suggestions on where to turn next? Are cross compilers the next
>> step?
>> >
>> > Try building with msys2, but make sure to use gcc/g++ from Rtools by
>> > setting the `CC` and `CXX` variables in the configure script. Cross
>> > compiling will make things even more complicated because binaries
>> > might not be compatible if your cross compiler has a different version
>> > of gcc or has been configured for another exception model (seh/drawf).
>> >
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