Good news everyone

[Ben Goodrich]

And by that, I actually mean good news, as far as making it possible to CRAN Stan.

http://dirk.eddelbuettel.com/blog/2013/01/31/#new_bh_package

Although they currently do Boost 1.51 and may need some input as to what all Stan would need.

Ben

[Jiqiang Guo]

They need a lot of input as to what all Stan need.  The package's size is less than those boost files we put in RStan.  For an example, tried to compile stanc in RStan.  This is the beginning of missing header files:

ccache g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG         -I"../inst/include/stansrc"   -I"../inst/include/stanlib/eigen_3.1.2"  -I"../inst/include/stanlib/eigen_3.1.2/unsupported"  -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/BH/include" -I"../inst/include"  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -O3       -c stanc.cpp -o stanc.o

In file included from ../inst/include/stansrc/stan/gm/compiler.hpp:4,

                 from stanc.cpp:5:

../inst/include/stansrc/stan/gm/ast.hpp:7:47: error: boost/variant/recursive_variant.hpp: No such file or directory

In file included from ../inst/include/stansrc/stan/gm/compiler.hpp:5,

                 from stanc.cpp:5:

../inst/include/stansrc/stan/gm/generator.hpp:4:43: error: boost/variant/apply_visitor.hpp: No such file or directory

In file included from ../inst/include/stansrc/stan/gm/compiler.hpp:6,

                 from stanc.cpp:5:

../inst/include/stansrc/stan/gm/parser.hpp:5:49: error: boost/fusion/include/adapt_struct.hpp: No such file or directory

../inst/include/stansrc/stan/gm/parser.hpp:6:45: error: boost/fusion/include/std_pair.hpp: No such file or directory

../inst/include/stansrc/stan/gm/parser.hpp:8:39: error: boost/spirit/include/qi.hpp: No such file or directory

--

Jiqiang

Ben

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[Daniel Lee]

Spirit is used for the compiler, stanc.

Hypothetically, could we compile the rest if we distributed stanc executables?

[Jiqiang Guo]

On Fri, Feb 1, 2013 at 10:25 AM, Daniel Lee <bea...@alum.mit.edu> wrote:

Spirit is used for the compiler, stanc.

Hypothetically, could we compile the rest if we distributed stanc executables?

Not now.  The models cannot be compiled either.  This can be easily tested in rstan:

> boost_lib <- system.file("include", package = 'BH')

> fit1 <- stan(model_code = scode, iter = 10, verbose = FALSE, boost_lib = boost_lib)

Error in compileCode(f, code, language = language, verbose = verbose) : 

  Compilation ERROR, function(s)/method(s) not created! In file included from /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstan/include/rstan/rstaninc.hpp:3,

                 from fileb725f5c2050.cpp:6:

/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstan/include/rstan/stan_fit.hpp:13:61: error: boost/random/additive_combine.hpp: No such file or directory

/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstan/include/rstan/stan_fit.hpp:15:39: error: boost/random/uniform_01.hpp: No such file or directory

/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstan/include/rstan/stan_fit.hpp:16:54: error: boost/random/uniform_real_distribution.hpp: No such file or directory

In file included from /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstan/include//stansrc/stan/math/matrix.hpp:14,

                 from /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rstan/include//stansrc/stan/io

[Ben Goodrich]

There is a note in TO-DO.txt about how to find which Boost files are necessary. We can talk about it with Dirk.

Ben

[Jiqiang Guo]

I did notice the note you put.  The boost files using that tool are a bit different from the brute force method I am using now, but I did not go ahead testing if that is also usable.  

But I do not know what we can talk about with BH package maintainers?  Are we going to ask them to include those specific files Stan needs? 

--

Jiqiang 

[Ben Goodrich]

On Friday, February 1, 2013 11:07:36 PM UTC-5, Jiqiang Guo wrote:

I did notice the note you put.  The boost files using that tool are a bit different from the brute force method I am using now, but I did not go ahead testing if that is also usable.  

But I do not know what we can talk about with BH package maintainers?  Are we going to ask them to include those specific files Stan needs? 

Yes, or at least part of them. If there is something Stan needs that is really unusual and Dirk doesn't want to put it in, then rstan could include that.

Ben