[Rcpp-devel] RInside under Windows
Patrick Burns
patrick at burns-stat.com
Thu Feb 16 17:43:49 CET 2012
On 16/02/2012 13:38, Dirk Eddelbuettel wrote:
>
> On 16 February 2012 at 11:00, Patrick Burns wrote:
> | Success.
>
> Nice.
>
> | I'll tentatively offer this summary of the
> | important things to do. There are three
> | environment variables to set:
>
> I should document some of this. Maybe in Makefile.win? Better ideas?
>
> | * PATH needs to include the path to the R DLLs
> | for example the bin\i386 under your R_HOME.
>
> Right. And I think there is little we can do -- the PATH has to be there for
> the dll files to be found so that the executable can run.
Yes, and I don't see that as being burdensome.
>
> | * R_HOME needs to be set.
>
> That one is odder. It definitely is found on Linux, and set. From my build
> directory:
>
> "R_HOME","/usr/lib64/R",
>
> Is R_HOME set inside your file RInsideEnvVars.h (which we generate during the
> build process). Maybe there is a bug there.
What I have there is:
"R_HOME","d:/Rcompile/recent/R-214~1.1",
and
"R_LIBS_USER","C:/Users/CRAN/Documents/R/win-library/2.14",
That R_HOME is certainly not going
to work on my machine. R_LIBS_USER
would be right for me if my name were
CRAN.
>
> | * R_LIBS_USER needs to be set. (Trying to do it
> | in .Rprofile didn't work for me.)
>
> Also not sure why .Rprofile doesn't work.
Far be it from me to screw anything up, but
perhaps others will have different results
anyway.
>
> | There is still a puzzle in my mind. Setting
> | R_LIBS_USER was necessary to get:
> | make -f Makefile.win
> | to work. Fine.
>
> Because we query Rcpp and RInside from R about their locations. So the
> location must be known.
>
> | But when it is not set and the exe files already
> | exist, there is strange (to me) behavior. Double
> | clicking runs the code, but running it in a
> | command window does not. Essentially R_LIBS_USER
> | is okay in the double click route but the environment
> | variable is necessary when run in a command window.
>
> Is that related to setting environment variables, and have it take effect
> only for new shells / command windows?
I think the explanation is that I made a
wrong assumption. I was so happy to have
it not crash that my definition of success
was probably a little weak. Doing the double
click means that the window disappears before
I can read it. So instead of having real
output it probably says Rcpp not found.
That is, I think things are fine -- the mystery
was inside my head rather than outside it.
Pat
>
> Dirk
>
> | Pat
> |
> | On 15/02/2012 14:03, Dirk Eddelbuettel wrote:
> |>
> |> On 15 February 2012 at 11:14, Patrick Burns wrote:
> |> | Dirk is once again correct. The "missing R.dll"
> |> | is a PATH problem.
> |> |
> |> | One way of solving it is to add the path to the
> |> | R DLLs to the end of PATH. For instance adding:
> |> |
> |> | C:\Program Files\R\R-2.14.1\bin\i386
> |> |
> |> | Once I've arranged those DLLs to be visible, the
> |> | new problem is:
> |> |
> |> | Fatal error: unable to open the base package
> |>
> |> If I recall correctly I solved that by setting R_HOME as
> |> your embedded R interpreter doesn't know its location...
> |>
> |> Dirk
> |>
> |> | That seems like it might be a path problem as well
> |> | but I'm not seeing how to fix it.
> |> |
> |> | Pat
> |> |
> |> | On 14/02/2012 21:52, Dirk Eddelbuettel wrote:
> |> |>
> |> |> On 14 February 2012 at 21:05, Patrick Burns wrote:
> |> |> | On 14/02/2012 20:59, Dirk Eddelbuettel wrote:
> |> |> |>
> |> |> |> (resending with CC to list which I omitted a minute ago --Dirk)
> |> |> |>
> |> |> |> On 14 February 2012 at 20:47, Patrick Burns wrote:
> |> |> |> |
> |> |> |> |
> |> |> |> | On 14/02/2012 20:14, Dirk Eddelbuettel wrote:
> |> |> |> |>
> |> |> |> |> On 14 February 2012 at 20:04, Patrick Burns wrote:
> |> |> |> |> | Obviously I don't *really* know what I'm
> |> |> |> |> | doing, or even *sort of* know what I'm
> |> |> |> |> | doing. But that never stopped me before.
> |> |> |> |> |
> |> |> |> |> | Here is hopefully enough breadcrumbs to
> |> |> |> |> | help someone, or even all of us.
> |> |> |> |> |
> |> |> |> |> |
> |> |> |> |> | I've reinstalled RInside so that I am
> |> |> |> |> | starting with the original Makefile.win
> |> |> |> |> |
> |> |> |> |> | *) There is an extraneous "n" on the first
> |> |> |> |> | line (first character) of Makefile.win -- 'make'
> |> |> |> |> | doesn't like that.
> |> |> |> |>
> |> |> |> |> I don't know for sure what your are talking about. A common fix would be to
> |> |> |> |> send a diff. Could you do that?
> |> |> |> |
> |> |> |> | This is Windows, remember -- perhaps there is a
> |> |> |>
> |> |> |> This is R, remember, and these tools come with Rtools by Duncan Murdoch.
> |> |> |>
> |> |> |> | way of doing a diff, I don't know it. But the
> |> |> |> | start of Makefile.win that I see out of the box is:
> |> |> |> |
> |> |> |> | n## -*- mode: makefile; tab-width: 8; -*-
> |> |> |> | ##
> |> |> |> | ## Simple Makefile for Windows
> |> |> |> |
> |> |> |> | Note the bizarre first character.
> |> |> |>
> |> |> |> Got it. Was still present here. Sorry about that, and thanks for catching it.
> |> |> |>
> |> |> |> Next release will fix, now corrected in SVN.
> |> |> |>
> |> |> |> |> | *) I need to comment out the command setting
> |> |> |> |> | R_HOME and set it in DOS instead.
> |> |> |> |>
> |> |> |> |> Works for me in the Makefile.win
> |> |> |> |>
> |> |> |> |> | *) The next problem is two instances each of:
> |> |> |> |> |
> |> |> |> |> | there is no package called [Rcpp, RInside]
> |> |> |> |> |
> |> |> |> |> | This is because .libPaths() is only finding
> |> |> |> |> | the main library and not the one where the
> |> |> |> |> | installed packages go.
> |> |> |> |> |
> |> |> |> |> | This is diagnosed by adding a line to Makefile.win:
> |> |> |> |> |
> |> |> |> |> | Rlibpaths := $(shell echo '.libPaths()' | $(R_HOME)/bin/R $(R_ARCH)
> |> |> |> |> | --vanilla --slave)
> |> |> |> |>
> |> |> |> |> I would recommend using ~/.Rprofile which strikes me as easier.
> |> |> |> |>
> |> |> |> |> | Adding a line to the checkR task:
> |> |> |> |> |
> |> |> |> |> | echo $(Rlibpaths)
> |> |> |> |> |
> |> |> |> |> | And then doing:
> |> |> |> |> |
> |> |> |> |> | make checkR -f Makefile.win
> |> |> |> |> |
> |> |> |> |> | This is the same in 32-bit and 64-bit.
> |> |> |> |> |
> |> |> |> |> | This problem can be remedied by setting the
> |> |> |> |> | R_LIBS_USER environment variable. You can
> |> |> |> |> | see what that is with the R command:
> |> |> |> |> |
> |> |> |> |> | Sys.getenv('R_LIBS_USER')
> |> |> |> |> |
> |> |> |> |> |
> |> |> |> |> | *) Now there is some progress, but not much.
> |> |> |> |> |
> |> |> |> |> | It compiles:
> |> |> |> |> | rinside_callbacks0
> |> |> |> |> | rinside_module_sample0
> |> |> |> |> | rinside_sample0
> |> |> |> |>
> |> |> |> |> Can you run rinside_sample0.exe ?
> |> |> |>
> |> |> |> Does that run?
> |> |> |
> |> |> | There is the missing R.dll problem.
> |> |>
> |> |> That is "just" a PATH problem. For now, copy this dll (and there will be
> |> |> four or five more from R, and then possibly from Rcpp and RInside) into a
> |> |> working (temp) directory and try.
> |> |>
> |> |> Seeing "hello, world" is a good proof. The rest is setup issues, which on
> |> |> Windows often descend into man-to-machine combat.
> |> |>
> |> |> Dirk
> |> |>
> |> |> |>
> |> |> |> |> | And gets an error on rinside_sample1:
> |> |> |> |> |
> |> |> |> |> | reopening rinside_sample1.exe: Permission denied
> |> |> |> |>
> |> |> |> |> Huh?
> |> |> |> |
> |> |> |> | Agreed. That is the only indication of it
> |> |> |> | being upset.
> |> |> |> |
> |> |> |> | But I renamed that file to try to make it do it last.
> |> |> |> | Running it again there was no error -- everything
> |> |> |> | compiled.
> |> |> |> |
> |> |> |> | Compiled for 32-bit.
> |> |> |> |
> |> |> |> | There is not an x64 subdirectory to 'lib' (as there is
> |> |> |> | with 'libs') so nothing compiles.
> |> |> |>
> |> |> |> Are you talking about RInside or Rcpp? Did you install from source or via
> |> |> |> the prebuilt CRAN binary?
> |> |> |>
> |> |> |> Everything from CRAN should now be multiarch, 32 and 64 bit.
> |> |> |
> |> |> | Prebuilt from CRAN. Rcpp is fine,
> |> |> | RInside/lib/x64 went AWOL.
> |> |> |
> |> |> | Pat
> |> |> |
> |> |> |>
> |> |> |> Dirk
> |> |> |>
> |> |> |> |> | However the three that did compile don't run. They
> |> |> |> |> | all have the error message:
> |> |> |> |> |
> |> |> |> |> | The program can't start because R.dll is missing from
> |> |> |> |> | your computer. Try reinstalling the program to fix
> |> |> |> |> | this problem.
> |> |> |> |>
> |> |> |> |> Could that be a Win7 security setting or something like it?
> |> |> |> |
> |> |> |> | That's an interesting idea. Anyone have
> |> |> |> | ideas about testing it?
> |> |> |> |
> |> |> |> | Pat
> |> |> |> |
> |> |> |> |>
> |> |> |> |> | This is using Rtools2.14 and R 2.14.1 with
> |> |> |> |> | RInside_0.2.6 Rcpp_0.9.9
> |> |> |> |>
> |> |> |> |> I think I used the same combination with success.
> |> |> |> |>
> |> |> |> |> Dirk
> |> |> |> |>
> |> |> |> |>
> |> |> |> |> | Pat
> |> |> |> |> |
> |> |> |> |> | On 14/02/2012 17:53, Dirk Eddelbuettel wrote:
> |> |> |> |> |>
> |> |> |> |> |> Hi Pat,
> |> |> |> |> |>
> |> |> |> |> |> On 14 February 2012 at 17:43, Patrick Burns wrote:
> |> |> |> |> |> | Good point about the Rtools version. I started
> |> |> |> |> |> | with 2.13, but I get the same thing with 2.14.
> |> |> |> |> |> |
> |> |> |> |> |> | Here are the key changes that I made to Makefile.win:
> |> |> |> |> |> |
> |> |> |> |> |> | RCPPINCL := -IC:/Users/pat/Documents/R/win-library/2.14/Rcpp/include
> |> |> |> |> |> | RCPPLIBS :=
> |> |> |> |> |> | C:/Users/pat/Documents/R/win-library/2.14/Rcpp/libs/i386/Rcpp.dll
> |> |> |> |> |> |
> |> |> |> |> |> | RINSIDEINCL := -IC:/Users/pat/Documents/R/win-library/2.14/RInside/include
> |> |> |> |> |> | RINSIDELIBS :=
> |> |> |> |> |> | C:/Users/pat/Documents/R/win-library/2.14/RInside/libs/i386/libRInside.dll
> |> |> |> |> |>
> |> |> |> |> |> That's not quite right, is it? What do (quoting from examples/standard/Makefile.win)
> |> |> |> |> |> these do:
> |> |> |> |> |>
> |> |> |> |> |> ## include headers and libraries for RInside embedding classes
> |> |> |> |> |> RINSIDEINCL := $(shell echo 'RInside:::CxxFlags()' | $(R_HOME)/bin/R $(R_ARCH) --vanilla --slave)
> |> |> |> |> |> RINSIDELIBS := $(shell echo 'RInside:::LdFlags()' | $(R_HOME)/bin/R $(R_ARCH) --vanilla --slave)
> |> |> |> |> |>
> |> |> |> |> |> | I then do:
> |> |> |> |> |> |
> |> |> |> |> |> | make -f Makefile.win
> |> |> |> |> |> |
> |> |> |> |> |> | I seem to have failed in my attempt to
> |> |> |> |> |> | tell it where R lives -- I get a cygwin
> |> |> |> |> |> | warning about MS-DOS style path, but I
> |> |> |> |> |> | don't think that is really a problem.
> |> |> |> |> |>
> |> |> |> |> |> R_HOME must be defined. You can get it from R, or hardcode it.
> |> |> |> |> |>
> |> |> |> |> |> The single best start is to try
> |> |> |> |> |>
> |> |> |> |> |> cd examples/standard
> |> |> |> |> |> make -f Makefile.win
> |> |> |> |> |>
> |> |> |> |> |> which should create 10+ executable. And you can borrow freely from that
> |> |> |> |> |> Makefile.win which should work.
> |> |> |> |> |>
> |> |> |> |> |> Lastly, the Cygwin thing is line noise which you can suppress by setting an
> |> |> |> |> |> env var appropriately. This comes from the newer Rtools.
> |> |> |> |> |>
> |> |> |> |> |> | It then attempts the g++ command, gives
> |> |> |> |> |> | the multiple definition statements, and:
> |> |> |> |> |>
> |> |> |> |> |> Linking is still wrong then.
> |> |> |> |> |>
> |> |> |> |> |> Dirk
> |> |> |> |> |>
> |> |> |> |> |>
> |> |> |> |> |
> |> |> |> |> | --
> |> |> |> |> | Patrick Burns
> |> |> |> |> | patrick at burns-stat.com
> |> |> |> |> | http://www.burns-stat.com
> |> |> |> |> | http://www.portfolioprobe.com/blog
> |> |> |> |> | twitter: @portfolioprobe
> |> |> |> |>
> |> |> |> |
> |> |> |> | --
> |> |> |> | Patrick Burns
> |> |> |> | patrick at burns-stat.com
> |> |> |> | http://www.burns-stat.com
> |> |> |> | http://www.portfolioprobe.com/blog
> |> |> |> | twitter: @portfolioprobe
> |> |> |>
> |> |> |
> |> |> | --
> |> |> | Patrick Burns
> |> |> | patrick at burns-stat.com
> |> |> | http://www.burns-stat.com
> |> |> | http://www.portfolioprobe.com/blog
> |> |> | twitter: @portfolioprobe
> |> |>
> |> |
> |> | --
> |> | Patrick Burns
> |> | patrick at burns-stat.com
> |> | http://www.burns-stat.com
> |> | http://www.portfolioprobe.com/blog
> |> | twitter: @portfolioprobe
> |>
> |
> | --
> | Patrick Burns
> | patrick at burns-stat.com
> | http://www.burns-stat.com
> | http://www.portfolioprobe.com/blog
> | twitter: @portfolioprobe
>
--
Patrick Burns
patrick at burns-stat.com
http://www.burns-stat.com
http://www.portfolioprobe.com/blog
twitter: @portfolioprobe
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