Read and Write MAT Files and Call MATLAB from Within R

Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.


News

Package: R.matlab

Version: 3.6.1 [2015-10-19] o ROBUSTNESS: Now readMat() detects when MAT v7.3 files are trying to be read and gives an informative error explaining those are not supported (Issue #23). Thanks to Thomas Beutlich (author of C library matio) for (non-official) pointers on how to distinguish MAT v5 from MAT v7.3 files.

Version: 3.6.0 [2015-07-05] o writeMat() gained argument 'fixNames=TRUE' for automatically replacing periods (.) in variable and field names with underscores (_). Thanks to Eugenio Piasini at University College London for suggesting this feature. o The MatlabServer.m script now outputs verbose/debug messages to standard error (or more precisely MATLAB file #2) (Issue #27). o Internal writeCommand() now gives an informative error if an unknown command is used. Previously it silently sent a "0L" command to MATLAB. o CLEANUP: Exporting only methods parts of the public API. o ROBUSTNESS: Increased test coverage to 87% (was 73%). o BUG FIX: writeMat() could not write logical elements. They are now converted to integers as MATLAB does not have a native logical / boolean data type. Previously, writeMat() silently ignored writing the data section of these logical elements resulting in a MAT file that could not be parsed by MATLAB (although readMat() could). Thanks to Eugenio Piasini for reporting on this problem.

Version: 3.5.1 [2015-03-27] o CRAN POLICIES/CLEANUP: Dropping reference to deprecated (soon defunct) utils::setInternet2() in help("Matlab").

Version: 3.5.0 [2015-03-05] o ROBUSTNESS: Now readMat() parses (effectively skips) also objects of array class mxOPAQUE_CLASS (=17). The official 'MAT-File Format R2015b' (Sept 2015) documentation does not describe this type. The parsing/skipping was done by reverse engineering and clever guesses. Thanks to GitHub user 'yakzan' for reporting on this type of MAT files. o CLEANUP: Internal fallback method for reading compressed MAT files using Omegahat's Rcompression package is not needed since R 2.10.0 and therefore dropped. o ROBUSTNESS: Package test coverage is 82%.

Version: 3.4.0 [2015-02-03] o ROBUSTNESS: Now readMat() parses also functional objects of array type (class) 16. Note that the official 'MAT-File Format R2015b' (Sept 2015) documentation does not describe this type. I had to implement the parser based on best guess on how the MAT file format works in general, so it might not work in all cases. Thanks to GitHub user 'anilatx' for reporting on this type of MAT files. o ROBUSTNESS: Now writeMat(pathname, ...) writes the MAT file atomically by first writing to a temporary file which is renamed only if successful. o ROBUSTNESS: Now writeMat() asserts that a maximum of 2^31-1 bytes are written per variable, otherwise an informative error is thrown. This byte limit is set by the MAT file format definition. Thanks to GitHub user 'intelinsight' for reporting on this. o ROBUSTNESS: Package test coverage is 81%.

Version: 3.3.0 [2015-09-22] o evaluate() gained argument 'capture' for capturing MATLAB output while evaluating MATLAB expressions. Thanks to Rohan Shah (GitHub user rohan-shah) for contributing code for this. o Explicit import of 'methods' and 'utils' functions. o ROBUSTNESS: Now the temporary filenames generated by MATLAB also includes the port number in addition to a semi-random sequence string. This should lower the risk for two MATLAB server using the same temporary filenames. o BUG FIX: readMat() gave an error when reading empty sparse matrices. Thanks to Gregory Jefferis at University of Cambridge for the bug report and bug fix.

Version: 3.2.0 [2015-02-24] o ROBUSTNESS: Package test coverage is 77%. o ROBUSTNESS: Now Matlab$startServer() always overwrites any existing 'MatlabServer.m' and 'InputStreamByteWrapper.class' to make sure the most recent versions are always used. Previously, existing files would be kept, requiring a manual removal in order to use more resent versions of these files. o BUG FIX: readMat(..., sparseMatrixClass='matrix') did not return the correct results in all cases. Added more package tests. o BUG FIX: readMat(..., sparseMatrixClass='SparseM') did not handle all-zero sparse matrices. Added package test for this. o BUG FIX: readMat(..., sparseMatrixClass='Matrix') would give "Error in validObject(.Object) : invalid class "dgCMatrix" object: lengths of slots 'i' and 'x' must match", whenever trying to read an sparse matrix with all zeros. Added package test for this case. Thanks to Abhinav Jauhri at Carnegie Mellon University for reporting on this and donating a test MAT file. o BUG FIX: Trying to retrieve a non-existing MATLAB variable using getVariable() would crash the R-to-MATLAB communication if remote=FALSE. Similarly, Trying to evaluate() a MATLAB expression that is invalid or by other means fails would also break the R-to-MATLAB bridge. The only solution is both cases was to restart R and MATLAB. Thanks to GitHub user badbye (yalei) for reporting on this.

Version: 3.1.1 [2014-10-10] o CRAN POLICIES/CLEANUP: Source code file InputStreamByteWrapper.java is no longer installed with this package. It is only the precompiled InputStreamByteWrapper.class file that is installed. Updated documentation accordingly. o Resubmitted to CRAN.

Version: 3.1.0 [2014-10-09] o Bumped up package dependencies. o Submitted to CRAN.

Version: 3.0.4 [2014-10-05] o BUG FIX: readMat() parsed an mxCELL_CLASS structure incorrectly if one of its names was empty. Thanks Dieter Menne at Menne Biomed Consulting in Germany for reporting on this.

Version: 3.0.3 [2014-07-24] o Added section on parallel MATLAB instances to help('Matlab').

Version: 3.0.2 [2014-06-22] o Added argument 'workdir' to Matlab$startServer() for setting the working directory of MATLAB. Thanks to Steven Jaffe at Morgan Stanley for the suggestion. o ROBUSTNESS: Under certain circumstances the MATLAB server script (MatlabServer.m) would try to access variables that were not yet defined. Thanks to Steven Jaffe at Morgan Stanley for spotting this.

Version: 3.0.1 [2014-05-18] o BUG FIX: Internal uncompressZlib() of readMat() opened several raw connections without closing them. Added system package test. Thanks Thilo Klein at University of Cambridge, UK, for the report.

Version: 3.0.0 [2014-05-06] o MAJOR: readMat() can now read all (zlib) compressed MAT files where it previously gave an error message on: "INTERNAL ERROR: Failed to decompress data [...] internal error -3 in memDecompress(2)".

Version: 2.4.0 [2014-04-29] o BUG FIX: When reading non-UTF-encoded strings (e.g. miUINT32), readMat() would drop any characters that were not in the ASCII set (0,32-127). This was overly conservative as it should at least have kept 7-bit ASCII characters (in 0-127), e.g. newline characters were dropped. This bug was introduced in R.matlab v1.2.0 (2008-02-12) when adding support for UTF-* strings via iconv(). Now we keep all 8-bit ASCII characters, which is also what the Matlab file format documentation suggests are used in non-UTF-encoded text matrices. Thanks to Steven Pav (San Francisco, CA) for reporting on this.

Version: 2.3.1 [2014-04-26] o Now package is byte-compiled by default. o SPEEDUP: MAT5 mxCHAR_CLASS structures are now read slighly faster.

Version: 2.3.0 [2014-02-21] o ROBUSTNESS: Now the package runs the garbage collector if unloaded in order to make sure finalize() is called on any deleted Matlab objects.

Version: 2.2.4 [2014-02-17] o BUG FIX: setOption() for Matlab gave ''Error in UseMethod("setOption") : no applicable method for 'setOption' applied to an object of class "c('Options', 'Object')"''. Added a package system test for this. Thanks to Griet Laenen at KU Leuven for reporting on this.

Version: 2.2.3 [2014-02-03] o BACKWARD COMPATIBILITY: The inference on the type of compression used in the error message when uncompression failed would itself generate an error on R (< 3.0.0). o Bumped up package dependencies.

Version: 2.2.2 [2014-01-28] o Added option 'R.matlab::readMat/v4/textMatrixCollapse' controlling whether MAT v4 text matrixes are collapsed into strings by row ("byrow"; default), by column ("bycolumn") or not at all ("none"). o Whenever there is an uncompress error in readMat(), it now tries to infer what type of compression the buffer has by inspecting the first two bytes and include the type in the error message. o BUG FIX: readMat(..., drop="singletonLists") would throw an error if the singleton list dropped contained NULL and that NULL was assigned to an element of an outer list, resulting in that element being dropped.

Version: 2.2.1 [2014-01-28] o ROBUSTNESS: Now Matlab$startServer() asserts that all MATLAB server files that are indeed successfully copied, iff missing. o CLEANUP: open() for Matlab no longer generates warnings on "socketConnection(...) ... cannot be opened", which occured while waiting/polling for the Matlab server to startup and respond.

Version: 2.2.0 [2014-01-21] o DOCUMENTATION: Updated list of Matlab versions for which the package has been confirmed to work with. o BUG FIX: The MatlabServer.m script would incorrectly consider Matlab v8 and above as Matlab v6. Thanks to Frank Stephen at NREL for reporting on this and providing a patch. o Bumped up package dependencies.

Version: 2.1.0 [2013-11-29] o CLEANUP: Now package only imports R.oo (no longer attaches it). Also, the package now imports R.utils (used to suggest and attach it when needed). These updates make the package more "silent". o CLEANUP: Dropped obsolete autoload():s. o Now the 'R.matlab' Package object is also available when the package is only loaded (but not attached). o ROBUSTNESS: Added package system test asserting that readMat() can be called without attaching the package.

Version: 2.0.7 [2013-11-28] o Now the 'INTERNAL ERROR' message readMat() throws on failed decompression also includes the first and last bytes of the data block that it tried to decompress. This will further help troubleshooting.

Version: 2.0.6 [2013-09-20] o ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().

Version: 2.0.5 [2013-09-16] o ROBUSTNESS: Added one explicit import from the 'utils' package.

Version: 2.0.4 [2013-09-11] o CONSISTENCY: Added argument 'drop' to readMat() to control how singleton dimensions of for instance nested lists are dropped or not. The defaults are now such that R.matlab v2.0.4 is consistent with R.matlab v1.7.1 (R.matlab v2.0.0-2.0.3 were not). Thanks to Claudia Beleites at IPHT Jena, Germany for reporting on this. o Bumped up package dependencies.

Version: 2.0.3 [2013-09-10] o WORKAROUND/BUG FIX: readMat() would an error when parsing an empty 'mxCHAR_CLASS' matrix with a 0x0 dimension. It is not clear whether this is a valid MAT v5 structure or not, but I've added a workaround. Thanks Claudia Beleites at IPHT Jena, Germany for reporting on this.

Version: 2.0.2 [2013-07-17] o DOCUMENTATION: Added section of '-v7.3' MAT files to help("readMat").

Version: 2.0.1 [2013-07-11] o Updated all documentation and messages to use 'MATLAB' instead of 'Matlab'. o Now the 'INTERNAL ERROR' message that people forward to the package maintainer also includes the version of the R.matlab package. o Bumped up package dependencies.

Version: 2.0.0 [2013-05-25] o SPEEDUP: Made readMat() significant faster. More than 15x speedup(!) is observed on MAT files with many small structures. This was achieved by (i) dramatically decreasing the amount of memory allocation and garbage collection needed by the internal raw buffer mechanism, by (ii) dropping an internal rm() calls that was called very often, as well as by (iii) minimizing the number of times local functions and objects are created. o Now readMat() also accepts a raw vector as input. o Now readMat() no longer generates warnings reporting on "In readBin( con = rawBufferT, what = what, size = size, n = n, signed = signed, : 'signed = FALSE' is only valid for integers of sizes 1 and 2." o DOCUMENTATION: Restructured help("readMat"). Added a section on 'Speed performance'.

Version: 1.7.1 [2013-05-20] o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

Version: 1.7.0 [2013-04-15] o readMat() now support reading 64-bit integers [array type (class) 'mxINT64_CLASS' and 'mxUINT64_CLASS'] on machines/versions of R with .Machine$sizeof.long >= 8 or .Machine$sizeof.longlong >= 8. o Package utilizes new startupMessage() of R.oo. o ROBUSTNESS: Now nearly all S3 methods are declared properly in the namespace.

Version: 1.6.4 [2013-03-08] o Added an [email protected] field to the DESCRIPTION. o DOCUMENTATION: Updated the help usage section for all static methods.

Version: 1.6.3 [2013-01-17] o Bumped up package dependencies.

Version: 1.6.2 [2012-12-02] o CLEANUP: R CMD check no longer warns on global assignments. o Bumped up package dependencies.

Version: 1.6.1 [2012-06-30] o Updated package dependencies.

Version: 1.6.0 [2012-06-07] o BUG FIX: readMat() could not read sparse matrices containing logical values, only numerics. This was because the 'logical' bit in the Array Flags was not utilized by readMat(), which in turn was because the file format documentation is rather vague on how to use that bit. This means that readMat() now represents sparse logical matrices using logical values, except when sparseMatrixClass="SparseM", because SparseM matrices can only hold numeric values. Thanks to Irtisha Sinhg at Cornell University for reporting on this.

Version: 1.5.9 [2012-05-05] o Now readMat() decompression error messages are more informative. o Now it is possible to specify the decompression method for readMat().

Version: 1.5.8 [2012-04-16] o Package now only imports R.methodsS3.

Version: 1.5.7 [2012-04-13] o The 'Rcompression' update in v1.5.5 introduced a bug, causing the loading of that package to fail.

Version: 1.5.6 [2012-04-02] o BUG FIX: readMat(..., verbose=-111) would give an error on object 'zraw' not being found.

Version: 1.5.5 [2012-04-01] o ROBUSTNESS: Move most of the test code that was in the examples of readMat() and writeMat() to formal system tests of the package, and made those examples simpler. o CLEANUP: Removed 'Rcompression' from set of "Suggests" packages, because since R v2.10.0 (Oct 2009) we can use memDecompress() of the 'base' package instead. However, just in case someone is still running older versions of R, readMat() does indeed still look for 'Rcompression' as a fallback.

Version: 1.5.4 [2012-03-06] o CRAN POLICY: Removed all internal copies of 'base' functions that have .Internal() calls.

Version: 1.5.3 [2011-12-08] o DOCUMENTATION: Added a section to help(Matlab) on how to connect through firewalls. Thanks Bas de Regt at University of Adelaide for the suggestion.

Version: 1.5.2 [2011-11-02] o CLEANUP: Fixed an R CMD check NOTE that would show up in R v2.15.0 devel.

Version: 1.5.1 [2011-09-27] o The version 1.5.0 that was submitted to CRAN did not include the adjustments for startup messages. Thus, resubmitting this one to CRAN. o Updated the R and package dependencies.

Version: 1.5.0 [2011-09-24] o GENERALIZATION: Now readMat() utilizes base::memDecompress() to uncompress compressed data structures, unless running R v2.9.x or before, in case Rcompression::uncompress() is used, iff installed. R v2.10.0 was released October 2009. Thanks Stephen Eglen at University of Cambridge for reminding me about memDecompress(). o CLEANUP: Now using packageStartupMessage() instead of cat().

Version: 1.4.0 [2011-07-25] o ROBUSTNESS: Added an example of verbose output to example(readMat). o Added a namespace to the package, which will be more or less a requirement in the next major release of R. o CLEANUP: Now all references to the Rcompression package is within the local uncompress() function of readMat(). This makes the code more modular making it easier to implement alternatives to Rcompression::uncompress().

Version: 1.3.7 [2011-02-01] o ROBUSTNESS: Now using argument 'imaginary' (not 'imag') in calls to complex().

Version: 1.3.6 [2010-10-29] o ROBUSTNESS: Now writeMat() gives an error if duplicated object names are used, e.g. writeMat(..., A=1, B=2, A=3). o ROBUSTNESS: Now writeMat() gives an error, not a warning, if there are non-named objects. o BUG FIX: The test for non-named objects to writeMat() did not work correctly. Thanks Claudia Beleites for the report.

Version: 1.3.5 [2010-10-28] o DOCUMENTATION: Clarified in the help of writeMat() that it can only write 'uncompressed' MAT files. o ROBUSTNESS: Although readMat() can read non-named objects, in Matlab it is only the 'load()' function call that can read it but not the plain 'load' call. Because of this, writeMat() will now give a warning if it detects non-named objects. For instance, in writeMat("foo.mat", x=a, y) the object 'a' is named (as "x") whereas 'y' is not. To name the objects and avoid the warning, use writeMat("foo.mat", x=a, y=y). Thanks Claudia Beleites at University of Trieste for reporting on this.

Version: 1.3.4 [2010-10-26] o DOCUMENTATION: Clarified and corrected some sentences in help(Matlab). o DOCUMENTATION: Added Matlab 7.11.0.584 (R2010b) to the list of confirmed version that are compatible with R.matlab. o BUG FIX: The MatlabServer.m script incorrectly referred to the InputStreamByteWrapper class as java.io.InputStreamByteWrapper. This hopefully solves previously reports on obtaining "??? Undefined variable "java" or class "java.io.InputStreamByteWrapper". Error in ==> MatlabServer at 262 reader = java.io.InputStreamByteWrapper(4096);". This bug was introduced in R.matlab v1.2.5 (2009-08-25). Thanks Kenvor Cothey at GMO LCC for reporting on this.

Version: 1.3.3 [2010-09-18] o BUG FIX: readMat() would throw an exception on 'Error in dim(matrix) <- dimensionsArray$dim : dims [product 1] do not match the length of object [0]' in rare cases related to empty strings. Not sure if those cases are legal, but added an ad hoc workaround for them. Thanks Claude Flene at University of Turku for reporting this.

Version: 1.3.2 [2010-08-28] o Now the MatlabServer script reports it's version when started. o DOCUMENTATION: Removed some minor ambiguities in help(Matlab) and updated example(Matlab) with some more troubleshooting statements. o DOCUMENTATION: Added Matlab 7.4.0 (R2007a), 7.7.0.471 (R2008b), and 7.10.0.499 (R2010a) to the list of confirmed version that are compatible with R.matlab. Thanks Ajay Tripathy at UC Berkeley and Marco Colombo at University of Edinburgh for reporting this. o BUG FIX: Now MatlabServer.m saves variables using the function form, i.e. save(). This solves the problem of having single quotation marks in the pathname. Thanks Michael Q. Fan at NC State University for reporting this problem.

Version: 1.3.1 [2010-04-20] o DOCUMENTATION: Minor update to argument 'fixNames' of help(readMat). Thanks Stephen Eglen (University of Cambridge) for the suggestion.

Version: 1.3.0 [2010-02-03] o GENERALIZATION: Now readMat() can read also nested miMATRIX structures. Issue reported by Jonathan Chard at Mango Solutions, UK.

Version: 1.2.6 [2009-10-16] o MEMORY OPTIMIZATION: For very large compressed data objects, there would not be enough memory to allocate the internal buffer resulting in an error. Before this buffer was initiated to be 10 times the size of the compressed data. If that fails, now readMat() tries smaller and smaller initial buffers, before giving in up. Also, it now starts with a buffer 3 (not 10) times the compressed size. Thanks to Michael Sumner for reporting this problem.

Version: 1.2.5 [2009-08-25] o BUG FIX: The Matlab server script (MatlabServer.m) gave the error "Undefined function or method 'ServerSocket' for input arguments of type 'double'.", when launching it via Matlab$startServer(). It seems like import java.net.* etc. does not work. A workaround is to specify the full path for all Java classes, e.g. java.net.ServerSocket. Thanks Nicolas Stadler for reporting this issue.

Version: 1.2.4 [2008-10-29] o If onWrite == NULL, then there is no longer an outer two-pass scan for figuring out the size of MAT structure. However, instead each internal writeDataElement() has to do a two-pass scan in order to figure out the number of bytes before writing each element. o BUG FIX: Arrays with more than two dimension would be written as vectors. Thanks Minho Chae for reporting this. o BUG FIX: From v1.2.2, writeMat() would generate corrupt MAT files. Reverted writeMat() back to v1.2.1 and updated as above.

Version: 1.2.3 [2008-07-20] o Updated example(readMat) so that it gives no error if the optional 'Rcompression' package is not installed.

Version: 1.2.2 [2008-07-12] o Now the first pass in writeMat() that counts the number of bytes to be written is skipped if argument 'onWrite' is not given. This means that writing to file, which is the most common use case, will no longer involve the counting. Thank to Adam Grossman at Stanford University for suggesting the modification and providing initial code. He reports a substantial speedup in writing large files (38MB file). o CLEAN UP: Removed internal debugging/asserting code. o Renamed the HISTORY file to NEWS.

Version: 1.2.1 [2008-05-08] o In readMat()/writeMat() we use an internal character vector to represent the 8-bit ASCII character set. However, in R one cannot represent ASCII 0x00 - it resolves to an empty string, and from R v2.8.0 we will get a warning if we try. For now, we have replaced the ASCII for 0x00 with the empty string (unless before R v2.6.0). We might want to move away from using this ASCII vector for intToChar()/charToInt() and instead make use of intToUtf8()/utf8ToInt() or alternatively just rawToChar()/charToRaw().

Version: 1.2.0 [2008-02-12] o Added support for reading compressed MAT files. It requires that the 'Rcompression' package (Omegahat.org) is available. o Added support for also returning sparse matrices according to the representations given by either the 'Matrix' or the 'SparseM' package. o Added simple UTF-* string support. Conversion should be accurate when the R installation supports iconv. o Added mat-files/StructWithSparseMatrix-v4.mat from JR. o Credits for all of the above new feature goes to Jason Riedy at the Computer Science Dept, UC Berkeley. Thanks also to Duncan Temple-Lang at UC Davis for the Rcompression package.

Version: 1.1.4 [2007-04-19] o Added a "hint" to error message 'Tag type not supported: miCOMPRESSED' to clarify that readMat() does not support compressed MAT files.

Version: 1.1.3 [2007-04-07] o Update so that package passes R CMD check R v2.5.0. o Replaced Sys.putenv() with new Sys.setenv() (to be deprecated in R v2.5.0).

Version: 1.1.3 [2006-12-28] o The example in help(Matlab) is now using default values for 'host' and 'port' making the example less confusing. o Now open() throws an error if connection to Matlab failed (before FALSE was returned). o Extended the accepted range of ports to [1023,66535]. o Added more details on available options in setOption() and how to avoid time outs.

Version: 1.1.2 [2006-05-08] o BUG FIX: When the port for the Matlab server (MATLABSERVER_PORT) was out of range, a Matlab syntax error occurred, i.e "... Line: 109 Column: 45 ")" expected, "identifier" found.'. Thanks Alexander Nervedi for reporting this.

Version: 1.1.1 [2006-01-21] o Added argument 'port' to Matlab$startServer(..., port=NULL) to start the Matlab server such that it listens to another port than the default 9999. Internally the server first tries to obtain the port number by environment variable 'MATLABSERVER_PORT'. This feature was requested by Wang Yu at Iowa State University. o Another version has been added to the list of Matlab versions that are confirmed to work with R.matlab. See ?Matlab.

Version: 1.1.0 [2005-06-29] o BUG FIX: Forgot to "implement" miSINGLE, i.e. to set 'knownTypes' and 'knownWhats' for this. Thanks to Craig Aumann for the report. o BUG FIX: readMat() did not read 'complex' matrices in MAT v5 correctly. Thanks again to Chris Sims for the bug report. o BUG FIX: readMat() did not read 'text' matrices in MAT v4 correctly. Thanks to Chris Sims, Princeton University, for for the patch. o If using the Matlab class, the package requires the R.utils where the classes Java and Verbose was moved. The methods for dealing with user options in the Matlab class are provided by the Options class also in R.utils. Similarly, if verbose != FALSE in readMat() or writeMat(), then the R.utils package is required.

Version: 1.0.3 [2005-05-26] o Added support for used defined options to Matlab objects via methods setOption() and getOption(). Current supported options are "readResult/maxTries" and "readResult/interval" to provide a "workaround" for the problem with timeout errors in evaluate(). Thanks Thomas Romary, France, for (re-)reporting this problem. o Added class Options. This will probably move to another package whenever it becomes stable and widely used.

Version: 1.0.2 [2005-05-03] o Now Matlab struct's are read into an R structure. o BUG FIX: Reading empty struct:s (and cells) tried to read one field because seq(0) and not seq(length=0) was used. Updated all occurrences of this problem. o Replaces package directory misc/ with two new directories mat-files/ and externals/.

Version: 1.0.1 [2005-04-08] o BUG FIX: readMat() failed to read some Matlab struct's because of a parsing error. o BUG FIX: Internally in readMat() - in readMat5DataStructure() it might be data readTag() returns a tag referring to a data block of zero length (nbrOfBytes == 0). Now list(NULL) is returned in this case. o BUG FIX: The MatlabServer script did (indeed) not work with Matlab v7; the wrong version was included. Thanks Patrick Drechsler, University of Wuerzburg for reporting the above two problems. o Minor additions to help pages.

Version: 1.0 [2005-02-25] o Moved to CRAN.

Version: 0.94 [2005-02-24] o Updated the MatlabServer.m script to automatically set the Java classpath for Matlab v7 and higher. This will assure that InputStreamByteWrapper.class is found as long as it is in the same directory as the *.m script. Thanks Yichun Wei at University of Southern California for suggesting this and also for suggesting additional help instructions. o Added a Wishlist and an Acknowledgements section to "about". o Added more information on how to start the Matlab server.

Version: 0.93 [2005-02-20] o Added autoload("hasVarArgs") to 000.R. o Updated the Matlab example to be more explicit about problems with Matlab$startServer() and Matlab v7.

Version: 0.92 [2005-02-17] o Package now passes R CMD check on R v2.1.0 devel without warnings. o Added appendVarArgs=TRUE to setMethodS3(), which specifies that '...' should be added, if missing. o Add argument '...' to all methods to make it even more consistent with any generic function. This is also done for a few methods in the R base packages. o BUG FIX: readMat() would not read non-signed bytes correctly.

Version: 0.91 [2005-02-11] o Package passes R CMD check on R v2.1.0 devel too. o Moved the Java class from R.io to this package, since it is currently only used here. It is used for reading and writing Java bytes, ints and (UTF) strings when communicating with Matlab. o Updated description of package. Preparing for moving to CRAN. o Added Rdoc comments to internal Verbose classes.

Version: 0.8 [2004-02-24] o Added a setVerbose() method to the Matlab class, which allows the user to get details at various levels of the Matlab process. o WORK AROUND: It sometimes happens that the reply from Matlab is not transferred "quick enough" and even if the connection should block we receive NULL giving an error. The work around for now is to try to read the answer again. The symptom was that an error in readResult() complain about "if (answer == 0)" where answer was of length 0. o Added support for reading sparse matrices. Sparse matrices are expanded to regular matrices, which means that some may be too large to be loaded. o BUG FIX: The header of MAT v4 files was not parsed correctly, which made MAT v4 files unrecognized and assumed to be MAT v5 files which in turn could not be read. o BUG FIX: Used "sparce" instead of "sparse" in MOPT[4] tag (MAT v4), which most likely would generate an error for such structure.

Version: 0.7 [2003-12-02] o BUG FIX: Introduced a bug that made files written with big endian not to work. The reason was that "<-" was used instead of "<<-" in one new method. I do not like "<<-", but that is how it works.

Version: 0.6 [2003-11-25] o Created an readMat() that can read both MAT v4 and MAT v5 files. The MAT v4 reader was kindly provided by Andy Jacobson at the Princeton University. o writeMat() was created for consistency, but it does only support MAT version 5. o Note that I have now chosen to rename readMAT() and writeMAT() to readMat() and writeMat(), respectively. This is in line with the RCC, cf. readHtml() instead of readHTML(). If you really need readMAT() and writeMAT() you can easily write your own wrappers.

Version: 0.5 [2003-04-04] o I forgot to remove some debug code that outputs information about the Description comment every time a MAT file is read. Removed.

Version: 0.4 [2003-01-16] o Now require(R.io) is loaded with the package and not when the first Matlab client/server method is called. The former approach was a little bit annoying. o BUG FIX: The Matlab client/server implementation was broken due to bugs introduced in the Java class of the R.io package. Correcting these bugs made the Matlab part work again.

Version: 0.3 [2002-11-11] o BUG FIX: readMAT() would not work because getBits() previously in package R.oo was removed. getBits() is now added as a local function inside readMAT(). o Made all methods \keyword{internal}.

Version: 0.2 [2002-10-23] o Upgraded to make use of Rx.oo.

Version: 0.1 [2002-09-03] o Initial methods are readMAT() and writeMAT() for reading and writing Matlab MAT file structures. o Initial class is Matlab, which provides static methods for communicating with running Matlab server. o Package created.

Reference manual

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install.packages("R.matlab")

3.6.2 by Henrik Bengtsson, a month ago


https://github.com/HenrikBengtsson/R.matlab


Report a bug at https://github.com/HenrikBengtsson/R.matlab/issues


Browse source code at https://github.com/cran/R.matlab


Authors: Henrik Bengtsson [aut, cre, cph] , Andy Jacobson [ctb] (Internal MAT v4 reader) , Jason Riedy [ctb] (Support for reading compressed files , sparse matrices and UTF-encoded strings.)


Documentation:   PDF Manual  


Task views: Numerical Mathematics


LGPL (>= 2.1) license


Imports methods, utils, R.methodsS3, R.oo, R.utils

Suggests Matrix, SparseM


Imported by NetworkToolbox, eemR, hNMF, lans2r, oXim, retistruct, scalpel, sisal.

Depended on by AnalyzeFMRI.

Suggested by DATforDCEMRI, SLOPE, fda, geometry, hyperSpec, poweRlaw.


See at CRAN