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

[Elliot Joel Bernstein]

John -

Thanks for the suggestions. I tried taking not only Rcpp but R out of the
loop, and just compiling from the command line with MinGW. That crashed as
well, so I think there's probably a compatibility issue with MATLAB's API
and MinGW. I'll contact Mathworks tech support to try and get some help
with that.

Regarding v7.3...my files aren't all v7.3, but I could definitely save them
all that way, which might be the easiest solution. I tried what you
suggested with some of my real data files, which contain two variables
each: a matrix and a struct. I get the following warnings:

> data <- h5dump("z:/temp/test73.mat", bit64conversion='double')
Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced
by NA's
Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced
by NA's
Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced
by NA's

The data look OK, as far as I can tell. (The matrix is 411x30927, so it's
not like I can check every element, but I don't see anything obviously
wrong.) In addition to the two variables I was expecting, the result has
two additional elements, #refs# and #subsystem. I'm not actually sure how
to see what they contain, since the names include the comment character.
Can I safely ignore those warnings?

Thanks.

- Elliot


On Wed, Mar 25, 2015 at 11:09 AM, John Buonagurio <jbuonagurio at exponent.com>
wrote:

> 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;
> > }
>
> --
> A man, a plan, a cat, a ham, a yak, a yam, a hat, a canal – Panama!
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