[Rcpp-devel] Bug: RcppArmadillo.package.skeleton builds faulty man/*.Rd files

Nathan VanHoudnos nathanvan at gmail.com
Thu Jul 12 17:18:23 CEST 2012

Hi Dirk,

Thanks for straightening me out about the documentation issues belonging to
base R instead of Rcpp. I should have checked that first.

And your point about inline not really being a "package-able" thing makes
sense. I was able to force my toy inlineExample package to install by

   1. using the `code_files` argument,
   2. deleting the `*.Rd` files in `man/` and
   3. modifying DESCRIPTION to include `inline` for `Depends:` and

But then when I fire up a session of R and try to use it:

> require(inlineExample)
Loading required package: inlineExample
Loading required package: Rcpp
Loading required package: RcppArmadillo
Loading required package: inline
> plus.two.cpp( matrix(1:12, ncol=3))
Error in .Primitive(".Call")(<pointer: (nil)>, UmatrixR) :
  NULL value passed as symbol address
> plus.two.cpp
An object of class "CFunc"
function (UmatrixR)
.Primitive(".Call")(<pointer: (nil)>, UmatrixR)
<environment: 0x2f28370>
Slot "code":
[1] "\n// includes from the plugin\n#include <RcppArmadillo.h>\n#include
<Rcpp.h>\n\n\n#ifndef BEGIN_RCPP\n#define BEGIN_RCPP\n#endif\n\n#ifndef
END_RCPP\n#define END_RCPP\n#endif\n\nusing namespace Rcpp;\n\n\n// user
includes\n\n\n// declarations\nextern \"C\" {\nSEXP file2f8c4cc10657( SEXP
UmatrixR) ;\n}\n\n// definition\n\nSEXP file2f8c4cc10657( SEXP UmatrixR
){\nBEGIN_RCPP\n\n  arma::mat U = Rcpp::as<arma::mat>(UmatrixR);\n

It fails. To my untrained eyes it seems that:

   1. the code that `inline` compiled never got copied by
   *.package.skeleton to the "right" part of the directory skeleton for later
   compilation by the R build process, and
   2. failing that the 'code_files' argument does not cause R to source
   those *.R files when the package is loaded.

Thinking about this further, it seems like (2) would be a really bad idea
because it would force the user to compile the code every time they loaded
their package. That would both exclude all users who require binary only
packages and just simply be really inefficient.

And (1) seems technically possible, but I don't know how involved that kind
of fix would be. I seems like a really low priority edge case. How often do
you have users who are sophisticated enough to try to make an R package
that don't know how to translate their `inline` script to the more robust R
build process? At least one! But probably not more than that...

So I'll post this as a question on stackexchange so that people can easily
find the answer.

Thanks for your help. Rcpp and its friends are really awesome. Thanks for
building them and supporting them!



On Wed, Jul 11, 2012 at 8:32 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

> Nathan,
> Two more comments. First, I am not sure you can even do what you did.
>  When I
> call Rcpp.armadillo.package() as (where I omit the R file argument -- no
> point including a file loading inline in a package, or redefining these
> functions)
> RcppArmadillo.package.skeleton(name='inlineExample',list=c('plus.two.cpp','plus.two.r'))
> I get
> R>
> RcppArmadillo.package.skeleton(name='inlineExample',list=c('plus.two.cpp','plus.two.r'))
> Creating directories ...
> Creating DESCRIPTION ...
> Creating NAMESPACE ...
> Creating Read-and-delete-me ...
> Saving functions and data ...
> Making help files ...
> Done.
> Further steps are described in './inlineExample/Read-and-delete-me'.
> Adding RcppArmadillo settings
>  >> added Depends: Rcpp, RcppArmadillo
>  >> added LinkingTo: Rcpp, RcppArmadillo
>  >> added useDynLib directive to NAMESPACE
>  >> added Makevars file with Rcpp settings
>  >> added Makevars.win file with RcppArmadillo settings
>  >> added example header file using Rcpp/RcppArmadillo
>  >> added example src file using armadillo classes
>  >> added example R file calling the C++ example
> Warning message:
> In dump(item, file = file.path(code_dir, sprintf("%s.R", list0[item]))) :
>   deparse of an S4 object will not be source()able
> R>
> indicating the result from cxxfunction() will not be representable. And
> indeed:
> edd at max:/tmp$ R CMD INSTALL inlineExample
> * installing to library ‘/usr/local/lib/R/site-library’
> * installing *source* package ‘inlineExample’ ...
> ** libs
> ccache g++-4.6 -I/usr/share/R/include -DNDEBUG
> -I"/usr/local/lib/R/site-library/Rcpp/include"
> -I"/usr/local/lib/R/site-library/RcppArmadillo/include"   -fpic  -g -O0
> -Wall -c rcpparma_hello_world.cpp -o rcpparma_hello_world.o
> g++-4.6 -shared -o inlineExample.so rcpparma_hello_world.o
> -L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp
> -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -llapack -lblas
> -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
> installing to /usr/local/lib/R/site-library/inlineExample/libs
> ** R
> Error in parse(outFile) : 3:21: unexpected '<'
> 2: structure(function (UmatrixR)
> 3: .Primitive(".Call")(<
>                       ^
> ERROR: unable to collate and parse R files for package ‘inlineExample’
> * removing ‘/usr/local/lib/R/site-library/inlineExample’
> edd at max:/tmp$
> That is is simply not supported. You have to subscribe your inline'd object
> by hand.
> Second, and as for the manual page leading to an error: we can reproduce
> that
> via
>   package.skeleton(name='pkgskelExample',list=c('plus.two.r'))
> which is free of any Rcpp-isms.  So this appears to be "simply" a bug in R.
> Dirk
> --
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

Nathan VanHoudnos
|- Statistics & Public Policy PhD student
|- Program for Interdisciplinary Education Research (PIER) Fellowship
|- Carnegie Mellon University
|- http://www.andrew.cmu.edu/user/nmv

"We may at once admit that any inference from the particular to the
 general must be attended with some degree of uncertainty, but this
 is not the same as to admit that such inference cannot be absolutely
 rigorous, for the nature and degree of the uncertainty may itself be
 capable of rigorous expression."  -- R.A. Fisher
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