gmane.comp.lang.r.rcpp

Re: Successful install of rcppbugs on Mac OS X 10.7

Dirk Eddelbuettel — 2012-05-25T16:36:37

On 25 May 2012 at 12:10, Steve Lianoglou wrote:
| Hi,
| 
| Thanks for the detailed instructions on getting gcc-4.6 cooking on the mac.
| 
| One question though -- I thought it was considered a "bad idea" to
| have R (and its libraries) compiled w/ different compilers.
| 
| You now have base R which was compiled w/ apple's gcc (4.2) as well as
| a slew of other "C-inside R packages," but you now also have rcppbugs
| (and maybe other ones you compile in the future) being built w/
| gcc-4.6
| 
| Isn't this a bad idea?

Non-issue to me as 

 - for example Debian simply 'rolls' versions, switching what gcc / g++ point
   to; and on the machine I type this it has been 4.6, 4.5, 4.4, 4.3 (?), 4.2
   and possibly also 3.4

 - yet R packages in /usr/local/lib/R/site-library are not recompiled and
   still work

 - exceptions to 'still work' comes only from R ("no NAMESPACE", new help
   format) and are rare

 - gcc / g++ 3.4 was explicitly designed to work interchangeably with the 4.*
   series 

 - even clang / cla

Re: Successful install of rcppbugs on Mac OS X 10.7

Steve Lianoglou — 2012-05-25T16:10:49

Hi,

Thanks for the detailed instructions on getting gcc-4.6 cooking on the mac.

One question though -- I thought it was considered a "bad idea" to
have R (and its libraries) compiled w/ different compilers.

You now have base R which was compiled w/ apple's gcc (4.2) as well as
a slew of other "C-inside R packages," but you now also have rcppbugs
(and maybe other ones you compile in the future) being built w/
gcc-4.6

Isn't this a bad idea?

-steve


On Fri, May 25, 2012 at 1:34 AM, Nick Matzke <matzke-TVLZxgkOlNX2fBVCVOL8/A< at >public.gmane.org> wrote:

Re: Successful install of rcppbugs on Mac OS X 10.7

Whit Armstrong — 2012-05-25T11:17:04

Congrats!

You might find these links useful.

Here is my presentation from R/Fin:
https://github.com/downloads/armstrtw/rcppbugs/rcppbugs.pdf

Also, here is another github project where I'm collecting rcppbugs examples:
https://github.com/armstrtw/rcppbugs.examples

And please post any bugs you find here:
https://github.com/armstrtw/rcppbugs/issues

-Whit



On Fri, May 25, 2012 at 1:34 AM, Nick Matzke <matzke< at >berkeley.edu> wrote:
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Successful install of rcppbugs on Mac OS X 10.7

Nick Matzke — 2012-05-25T05:34:04

Hi all,

Thanks for your help (Whit especially) on various things. 
After a fair bit of effort I got rccpbugs installed on my 
Mac 10.7 in R.app.  Here's my setup:

 > sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] 
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     grDevices utils     datasets  graphics 
methods   base

other attached packages:
[1] rcppbugs_0.1.0        RcppArmadillo_0.3.0.2 Rcpp_0.9.10 
           inline_0.3.8

loaded via a namespace (and not attached):
[1] compiler_2.14.1 tools_2.14.1





The basic steps:

1. Install dependencies
install.packages("Rcpp")
install.packages("inline")

2. (I updated Xcode to 3.2 and installed the Command Line 
Tools, I doubt the details of this matter though.)

3. The default compiler on Mac OS X 10.7 is gcc4.2. 
However, rcppbugs needs gcc4.6.  I got gcc4.6 to install by 
following the directions here:

http://solarianprogrammer.com/2011/12/01/comp

Re: Specifying compiler to use within Rcpp

Dirk Eddelbuettel — 2012-05-25T00:33:45

Hi Nick,

On 24 May 2012 at 16:34, Nick Matzke wrote:
| I've got Mac OS X 10.7, which still uses gcc4.2.  I can 
| install a separate copy of a newer gcc (e.g. 4.7), but is 
| there a way to make Rcpp (and inline) use it while compiling?
| 
| I suppose I could use a symbolic link to make gcc refer to 
| gcc4.7 everywhere on my system, but that seems like an 
| inflexible solution.

That is a generic Unix / R question, not specific to Rcpp. You can either
deal with this system-wide, or just for R. What I do is to modify

     ~/.R/Makevars

where you set essentially every variable known to R -- see its
$RHOME/etc/Makeconf for inspiration.  I include my copy below; you see how I
switch compiler versions and also have a (currently commented-out) portion
for clang/clang++ from llvm.  Also note my use of ccache which is very
helpful.


On 24 May 2012 at 19:42, Whit Armstrong wrote:
| For mac specific questions, you should also try here:
| https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Not a Mac-specific questi

Re: Specifying compiler to use within Rcpp

Whit Armstrong — 2012-05-24T23:42:00

For mac specific questions, you should also try here:
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Also, you might want to stick w/ gcc 4.6.

gcc 4.7 is still very new, and I have already seen issues w/ cppbugs
when -O2 is turned on...

just my 2c.

-Whit


On Thu, May 24, 2012 at 7:34 PM, Nick Matzke <matzke< at >berkeley.edu> wrote:
_______________________________________________
Rcpp-devel mailing list
Rcpp-devel< at >lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

Specifying compiler to use within Rcpp

Nick Matzke — 2012-05-24T23:34:53

Hi,

I've got Mac OS X 10.7, which still uses gcc4.2.  I can 
install a separate copy of a newer gcc (e.g. 4.7), but is 
there a way to make Rcpp (and inline) use it while compiling?

I suppose I could use a symbolic link to make gcc refer to 
gcc4.7 everywhere on my system, but that seems like an 
inflexible solution.

Any help appreciated.  Cheers!
Nick

Rcpp modules documentation

Dirk Eddelbuettel — 2012-05-24T19:44:23

There had been a number of posts over the last few weeks (months?) where
folks were struggling with getting Rcpp modules going based on the examples
in the vignette.  

I just spent a few hours cleaning things up.  The gist of it is

  -- this always worked, but I often forgot to point out that loading
     a module is different when you use inline to compile/load on the fly,
     and when you use a package;

  -- both uses were in fact documented in the vignette;

  -- both uses were in fact used in the unit tests too;

but it was a little hard to get to.  Now with the cleanup:: 

  -- the unit test for Rcpp modules actually had three different modules which
     I commented a bit more, and also moved to the package created by

        Rcpp.package.skeleton("somePackageName, module=TRUE)

     to provide more direct examples

  -- I moved some things from the 'evaluate but do not show' mode of Sweave
     into full view, so the vignette should be a tad more helpful as well.


So in short, "on the fly" and

Re: Another rcpp package for examples

Dirk Eddelbuettel — 2012-05-24T18:57:59

On 24 May 2012 at 15:58, Peter deVoil wrote:
| > | particular nastiness involved on windows platforms as the model is
| > | built with MSVC, yet calls GCC code (ie Rcpp) via extern "C".
| >
| > This comes up every now and then, and folks would surely love to see a good
| > tutorial and walk-through.
| 
| I'll have a go at it. Don't know how I'll go with the "good" part though.

Great.
 
| I used the windows dlsym() equivalent to call in to a handful of entry
| points. Given that this forces you to use C datatypes, you get none of
| the C++ operators that make Rcpp so useful - but in my case, the data
| exchange is fairly coarse and predictable.

Oh, so it is 

  a) really limited to atomistic C types just like the old .C() interface

  b) also highly non-portable as it will work only on that one platform.

Still, some people will want to try it regardless so it would be nice to have
some more documentation.

Dirk

Re: What is the best way of handling default arguments.

Dirk Eddelbuettel — 2012-05-24T18:53:02

On 24 May 2012 at 12:34, Andrew Redd wrote:
| Rcpp List,
| 
| Is there a recommended way to handle default arguments for
| constructors?  I have a class that I have created and exposed through
| Rcpp Modules.   I now found that I need to expose a tuning parameter
| and need to modify my constructors.   The standard way would be to
| include just a default argument, but I didn't think that Rcpp could
| handle default arguments in constructors.    Am I wrong?  Any
| recommendations?

I think you are correct.  

So you may have to make do with just setting a default value in the existing
constructor's body, and offering an additional setter.

Rcpp modules are a sort-of half-way house between the full glory of C++ and
the more direct interactive nature of R. Not everything can be mapped that
way, and we point to class member functions by name only.

Dirk

What is the best way of handling default arguments.

Andrew Redd — 2012-05-24T18:34:20

Rcpp List,

Is there a recommended way to handle default arguments for
constructors?  I have a class that I have created and exposed through
Rcpp Modules.   I now found that I need to expose a tuning parameter
and need to modify my constructors.   The standard way would be to
include just a default argument, but I didn't think that Rcpp could
handle default arguments in constructors.    Am I wrong?  Any
recommendations?

Thanks,
Andrew

Re: Another rcpp package for examples

Peter deVoil — 2012-05-24T05:58:50

I'll have a go at it. Don't know how I'll go with the "good" part though.

I used the windows dlsym() equivalent to call in to a handful of entry
points. Given that this forces you to use C datatypes, you get none of
the C++ operators that make Rcpp so useful - but in my case, the data
exchange is fairly coarse and predictable.

Yours,
pdev

Re: Another rcpp package for examples

Dirk Eddelbuettel — 2012-05-23T12:36:52

Hi Peter,

Thanks for announcing this here.  Always nice to hear about use cases
involving Rcpp and RInside.

On 23 May 2012 at 16:09, Peter deVoil wrote:
| Folks,
| 
| May I thank the Rcpp community for providing such a useful package.
| 
| For your records, may I let you know that the farming systems model
| APSIM (www.apsim.info) is using Rcpp/RInside as a wrapper around the R
| language; allowing snippets of R code to interact with apsim
| simulations. http://www.apsim.info/Wiki/RComponent.ashx has a brief
| outline.
| 
| Source code is available from
| http://apsrunet.apsim.info/svn/apsim/trunk/Model/RLink/. There is
| particular nastiness involved on windows platforms as the model is
| built with MSVC, yet calls GCC code (ie Rcpp) via extern "C".

Thanks for pointing to the SVN views. 

There are a few pages on the site that are a bit more restrictive:

   http://www.apsim.info/Wiki/Downloads.ashx
   http://www.apsim.info/Wiki/Access-to-APSIM.ashx

and I am not too sure how/if you can really do that i

Re: Another rcpp package for examples

Smith, Dale — 2012-05-23T11:44:25

"There is particular nastiness involved on windows platforms as the
model is built with MSVC, yet calls GCC code (ie Rcpp) via extern "C"."

I was not aware this particular nastiness was possible. At some point
I'll look at your code to see what it's doing. This particular nastiness
may actually simplify what I've got to do for the second part of our big
project.

Thanks,
Dale Smith, Ph.D.
Senior Financial Quantitative Analyst
Risk & Compliance
Fiserv.
107 Technology Park
Norcross, GA 30092
Office: 678-375-5315
Mobile: 678-982-6599
Mail: dale.smith-w4St3Zw4a6HQT0dZR+AlfA< at >public.gmane.org
www.fiserv.com

-----Original Message-----
From: rcpp-devel-bounces-ugOZBs531Z6LQD+cx0UyZNtNOq5v9fdn< at >public.gmane.org
[mailto:rcpp-devel-bounces-ugOZBs531Z6LQD+cx0UyZNtNOq5v9fdn< at >public.gmane.org] On Behalf Of Peter
deVoil
Sent: Wednesday, May 23, 2012 2:10 AM
To: rcpp-devel-ugOZBs531Z6LQD+cx0UyZNtNOq5v9fdn< at >public.gmane.org
Subject: [Rcpp-devel] Another rcpp package for examples

Folks,

May I thank the Rcpp community for pro

Another rcpp package for examples

Peter deVoil — 2012-05-23T06:09:57

Folks,

May I thank the Rcpp community for providing such a useful package.

For your records, may I let you know that the farming systems model
APSIM (www.apsim.info) is using Rcpp/RInside as a wrapper around the R
language; allowing snippets of R code to interact with apsim
simulations. http://www.apsim.info/Wiki/RComponent.ashx has a brief
outline.

Source code is available from
http://apsrunet.apsim.info/svn/apsim/trunk/Model/RLink/. There is
particular nastiness involved on windows platforms as the model is
built with MSVC, yet calls GCC code (ie Rcpp) via extern "C".

Thanks again,
Yours,
PdeV

Re: Problem with RInside "hello world" example

Dirk Eddelbuettel — 2012-05-22T20:11:29

On 22 May 2012 at 12:51, Michael Hannon wrote:
| Dirk Eddelbuettel <edd-8fiUuRrzOP0dnm+yROfE0A< at >public.gmane.org> wrote:
| 
| > On 22 May 2012 at 01:04, Michael Hannon wrote:
| >| Darren Cook <darren-BZBlJWF2IJvYtjvyW6yDsg< at >public.gmane.org> wrote:
| >|
| >| >> I've run into a problem with the RInside "hello world" > example.  I can
| >| >> not get it to compile on my system.  The first of the many error
| >| >> messages is:
| >| >>
| >| >>     undefined reference to `RInside::RInside(int, char const* const*,
| >bool)
| >| >
| >| > You are not telling g++ where to find the R libraries that you need to
| >| > link with.
| >
| >Correct -- the RInside package comes with four example directories.
| >
| >And each of these four directories has a Makefile.  The easiest to start with
| >is
| >
| >   examples/standard/Makefile
| >
| >as you can simply drop in a new file 'myhelloworld.cpp' (or any other name
| >you choose) into this directory and say 'make myhelloworld' --- and the
| >binary 'myhelloworld' wil

Re: Problem with RInside "hello world" example

Michael Hannon — 2012-05-22T19:51:12

  
Hmm.  Thanks, Dirk.  That Makefile is downright spooky smart (and worth a
study in its own right).  I was unaware of the "RHOME" option for R and the
"shell" function in GNU make.  Given that I had only one *.cpp file in the
directory, I got the binary to build simply by typing "make", but I did check
that "make <filename>" also appears to work.

Re: Problem with RInside "hello world" example

Dirk Eddelbuettel — 2012-05-22T10:19:57

On 22 May 2012 at 01:04, Michael Hannon wrote:
| Darren Cook <darren-BZBlJWF2IJvYtjvyW6yDsg< at >public.gmane.org> wrote:
| 
| >> I've run into a problem with the RInside "hello world" > example.  I can
| >> not get it to compile on my system.  The first of the many error
| >> messages is:
| >>
| >>     undefined reference to `RInside::RInside(int, char const* const*, bool)
| >
| > You are not telling g++ where to find the R libraries that you need to
| > link with.

Correct -- the RInside package comes with four example directories.

And each of these four directories has a Makefile.  The easiest to start with is

   examples/standard/Makefile

as you can simply drop in a new file 'myhelloworld.cpp' (or any other name
you choose) into this directory and say 'make myhelloworld' --- and the
binary 'myhelloworld' will be created for you.

It does this by querying R via Rscript to learn about 

   headers and libraries for R

   headers and libraries for Rcpp

   headers and libraries for RInside

and all six

Re: Problem with RInside "hello world" example

Michael Hannon — 2012-05-22T08:04:31


Thanks, Darren.  I think that must be the issue.  I'll try adding the
additional include/library directories later today.

For the record, it occurred to me that I didn't include any R, Rcpp, or
RInside information in my original post.  I've appended it below.

Re: Problem with RInside "hello world" example

Darren Cook — 2012-05-22T07:40:13

You are not telling g++ where to find the R libraries that you need to
link with.

I've a similar basic RInside example and I've got a comment in the
header that says compile it with this:

g++ -I/usr/local/lib/R/site-library/Rcpp/include
-I/usr/local/lib/R/site-library/RInside/include -I/usr/share/R/include
-L/usr/lib64/R/lib -lR -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp
-L/usr/local/lib/R/site-library/RInside/lib -lRInside
-Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -lRInside
-Wl,-rpath,/usr/local/lib/R/site-library/RInside/lib main.cpp


You may have to adjust the paths (I'm on ubuntu 10.04, and I think
default locations for all R packages), but it gives you an idea of what
you're missing.

Darren

P.S. In that same directory I've also a rather long Makefile that
describes itself as a "simple Makefile". It doesn't look like I wrote
it; I guess it is from the RInside examples or vignette.

Problem with RInside "hello world" example

Michael Hannon — 2012-05-22T07:29:43

Greetings.  I'm trying to go through some of the examples in the notes from
Dirk's Rcpp Masterclass of 28 April 2011.  (I didn't take the class.  I just
found the notes on the Internet.  Please let me know if my use of them
violates some law or protocol.  In case it makes any difference, I'm not
making any money from this project.)

I've run into a problem with the RInside "hello world" example.  I can not
get it to compile on my system.  The first of the many error messages is:

    undefined reference to `RInside::RInside(int, char const* const*, bool)

I've appended the details.  I get the same error if I omit the reference to
the c++0x standard.  What am I missing?

Thanks,