[Rcpp-devel] R.e. Using Rcpp and MATLAB MAT-File API to Read MAT Files

[John Buonagurio]

Elliot,

How are you building the executable? Did you make sure to include all dependencies in the search path (run depends.exe against libmat.dll and libmx.dll)? Did you make sure to set the appropriate architecture e.g. -m64 in CFLAGS? I don't have access to the MAT-File libraries to test this myself.

Start simple and take Rcpp out of the equation. Call matOpen from a simple C function with type void. Does it work with dyn.load() and .C()?

If you are *only* working with v7.3 files which are based on HDF5, you may be able to avoid this issue and access them using rhdf5: 

source("http://bioconductor.org/biocLite.R")
biocLite("rhdf5")
library(rhdf5)
h5dump("file.mat", load=FALSE)

John

From: rcpp-devel-bounces at lists.r-forge.r-project.org [mailto:rcpp-devel-bounces at lists.r-forge.r-project.org] On Behalf Of Elliot Joel Bernstein
Sent: Wednesday, March 25, 2015 9:28 AM
To: Dale Smith
Cc: xian at unm.edu; rcpp-devel at lists.r-forge.r-project.org
Subject: Re: [Rcpp-devel] R.e. Using Rcpp and MATLAB MAT-File API to Read MAT Files

Dale -

Thank you for the suggestion. I have MATLAB and the MATLAB libraries, and I am not looking to redistribute anything. I just have a lot of data in MAT files that I would like to be able to load analyze in R. I am able to compile and link against the MATLAB libraries, but the code crashes when I run it. I looked into the Octave FAQ. It looks like they don't handle v7.3 files either, and I don't think they provide an API that I could access from R/C++.

- Elliot

On Wed, Mar 25, 2015 at 8:36 AM, Dale Smith <DSmith at nexidia.com> wrote:
mat.h is a header file which comes with MATLAB. I don't think the license allows redistribution, and you would not be able to compile without the MATLAB libraries.

An alternative may be Octave since it will read .mat files. Perhaps someone can email the name of the header file used from the Octave distribution?

http://stackoverflow.com/questions/9915658/how-do-you-open-mat-files-in-octave

This also offers a viable way to test this type of code for those who don't have MATLAB.

Dale Smith, Ph.D. | Data Scientist | nexidia | office: +1 404 495 7220 ext 4008 | fax: +1 404 495 7221 | nexidia.com


-----Original Message-----
From: rcpp-devel-bounces at lists.r-forge.r-project.org [mailto:rcpp-devel-bounces at lists.r-forge.r-project.org] On Behalf Of Christian Gunning
Sent: Wednesday, March 25, 2015 8:08 AM
To: rcpp-devel at lists.r-forge.r-project.org
Subject: [Rcpp-devel] R.e. Using Rcpp and MATLAB MAT-File API to Read MAT Files

Can you provide a link to the mat.h file referenced in the source (which I assume is the same as the API mentioned below)?

Also, see Dirk's comments about compilers here:
http://stackoverflow.com/questions/10723165/using-visual-c-with-r
and here:
dirk.eddelbuettel.com/code/rcpp/Rcpp-FAQ.pdf

Best,
Christian

> I'm trying to use the MATLAB Mat-File API to read data from MAT files
> into R. (I've tried using the R.matlab package, but the matrices I'm
> loading can be very large, and that method was too slow. In addition,
> some of the files I'm loading are v7.3 MAT files, which are not
> supported by the package.) I wrote the following simple function to
> start testing. It works fine if I compile without the Rcpp parts in
> Visual Studio (i.e. I can call matOpen and get a nonzero pointer), but
> when I run in R it crashes my R session without displaying "Test".
>
> #include <Rcpp.h>
> #include "mat.h"
>
> using namespace Rcpp;
>
> // [[Rcpp::export]]
> NumericVector rcpp_mat_load() {
>
>     MATFile* mf = matOpen("z:/temp/test.mat", "r");
>     printf("Test\n");
>     double val = 10;
>     NumericVector y = NumericVector::create(val);
>     return y;
> }

--
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