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

Wed Mar 25 17:57:51 CET 2015

John -

One quick follow-up about the warnings: I think they have to do with
loading cell arrays. Basically, all the actual data ends up in the #refs#
field, in what seems like an arbitrary order, and the field that should
contain the data is all NAs. Do you know if there's any way to get around
that? I think all the cell arrays being saved contain only strings, so I
can change things in MATLAB to save them as char arrays if necessary.

Thanks.

- Elliot

On Wed, Mar 25, 2015 at 12:26 PM, Elliot Joel Bernstein <ejb6 at cornell.edu>
wrote:

> 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!
>> _______________________________________________
>> 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
>> _______________________________________________
>> 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
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20150325/1e3e67d5/attachment.html>