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: 3.6.2 [2017-09-26]

BUG FIXES:

  • Matlab$getOption() produced "Error in base::getOption(...) : 'x' must be a character string" in R-devel (to become R 3.6.0). Thank you Kurt Hornik for the troubleshooting and the fix.

CODE REFACTORING:

  • CLEANUP: Drop code conditional on non-supported old versions of R.

Version: 3.6.1 [2016-10-19]

NEW FEATURES:

  • 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 [2016-07-05]

NEW FEATURES:

  • 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.

  • The MatlabServer.m script now outputs verbose/debug messages to standard error (or more precisely MATLAB file #2) (Issue #27).

  • Internal writeCommand() now gives an informative error if an unknown command is used. Previously it silently sent a "0L" command to MATLAB.

SOFTWARE QUALITITY:

  • Increased test coverage to 87% (was 73%).

BUG FIXES:

  • 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.

DEPRECATED AND DEFUNCT:

  • CLEANUP: Exporting only methods parts of the public API.

Version: 3.5.1 [2016-03-27]

DOCUMENTATION:

  • Dropping reference to deprecated utils::setInternet2() in help("Matlab").

Version: 3.5.0 [2016-03-05]

NEW FEATURES:

  • 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.

SOFTWARE QUALITITY:

  • Package test coverage is 82%.

CODE REFACTORING:

  • 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.

Version: 3.4.0 [2016-02-03]

NEW FEATURES:

  • 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.

  • ROBUSTNESS: Now writeMat(pathname, ...) writes the MAT file atomically by first writing to a temporary file which is renamed only if successful.

  • 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.

SOFTWARE QUALITITY:

  • Package test coverage is 81%.

Version: 3.3.0 [2015-09-22]

NEW FEATURES:

  • 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.

  • 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.

BUG FIXES:

  • readMat() gave an error when reading empty sparse matrices. Thanks to Gregory Jefferis at University of Cambridge for the bug report and bug fix.

CODE REFACTORING:

  • Explicit import of 'methods' and 'utils' functions.

Version: 3.2.0 [2015-02-24]

NEW FEATURES:

  • 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.

BUG FIXES:

  • readMat(..., sparseMatrixClass='matrix') did not return the correct results in all cases. Added more package tests.

  • readMat(..., sparseMatrixClass='SparseM') did not handle all-zero sparse matrices. Added package test for this.

  • 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.

  • 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 the report.

SOFTWARE QUALITITY:

  • Package test coverage is 77%.

Version: 3.1.1 [2014-10-10]

CODE REFACTORING:

  • 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.

Version: 3.1.0 [2014-10-09]

CODE REFACTORING:

  • Bumped package dependencies.

Version: 3.0.4 [2014-10-05]

BUG FIXES:

  • 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]

DOCUMENTATION:

  • Added section on parallel MATLAB instances to help('Matlab').

Version: 3.0.2 [2014-06-22]

NEW FEATURES:

  • Added argument 'workdir' to Matlab$startServer() for setting the working directory of MATLAB. Thanks to Steven Jaffe at Morgan Stanley for the suggestion.

  • 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]

BUG FIXES:

  • 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]

SIGNIFICANT CHANGES:

  • 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]

BUG FIXES:

  • 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]

NEW FEATURES:

  • SPEEDUP: MAT5 mxCHAR_CLASS structures are now read slighly faster.

CODE REFACTORING:

  • Now package is byte-compiled by default.

Version: 2.3.0 [2014-02-21]

BUG FIXES:

  • 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]

BUG FIXES:

  • 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]

BUG FIXES:

  • 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).

CODE REFACTORING:

  • Bumped package dependencies.

Version: 2.2.2 [2014-01-28]

NEW FEATURES:

  • 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").

  • 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.

BUG FIXES:

  • 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]

NEW FEATURES:

  • ROBUSTNESS: Now Matlab$startServer() asserts that all MATLAB server files that are indeed successfully copied, iff missing.

  • 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]

DOCUMENTATION:

  • Updated list of MATLAB versions for which the package has been confirmed to work with.

BUG FIXES:

  • 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.

CODE REFACTORING:

  • Bumped package dependencies.

Version: 2.1.0 [2013-11-29]

NEW FEATURES:

  • Now the 'R.matlab' Package object is also available when the package is only loaded (but not attached).

  • ROBUSTNESS: Added package system test asserting that readMat() can be called without attaching the package.

CODE REFACTORING:

  • Package now 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".

  • Dropped obsolete autoload():s.

Version: 2.0.7 [2013-11-28]

NEW FEATURES:

  • 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]

CODE REFACTORING:

  • ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().

Version: 2.0.5 [2013-09-16]

CODE REFACTORING:

  • ROBUSTNESS: Added one explicit import from the 'utils' package.

Version: 2.0.4 [2013-09-11]

NEW FEATURES:

  • 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.

  • Bumped package dependencies.

Version: 2.0.3 [2013-09-10]

BUG FIXES:

  • readMat() would produce 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]

DOCUMENTATION:

  • Added section of '-v7.3' MAT files to help("readMat").

Version: 2.0.1 [2013-07-11]

NEW FEATURES:

  • Now the 'INTERNAL ERROR' message that people forward to the package maintainer also includes the version of the R.matlab package.

DOCUMENTATION:

  • Updated all documentation and messages to use 'MATLAB' instead of 'Matlab'.

CODE REFACTORING:

  • Bumped package dependencies.

Version: 2.0.0 [2013-05-25]

SIGNIFICANT CHANGES:

  • 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.

NEW FEATURES:

  • Now readMat() also accepts a raw vector as input.

  • 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."

DOCUMENTATION:

  • Restructured help("readMat"). Added a section on 'Speed performance'.

Version: 1.7.1 [2013-05-20]

DOCUMENTATION:

  • Now all Rd \usage{} lines are at most 90 characters long.

Version: 1.7.0 [2013-04-15]

NEW FEATURES:

  • 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.

  • Package utilizes new startupMessage() of R.oo.

CODE REFACTORING:

  • Nearly all S3 methods are now declared properly in the namespace.

Version: 1.6.4 [2013-03-08]

DOCUMENTATION:

  • Updated the help usage section for all static methods.

CODE REFACTORING:

Version: 1.6.3 [2013-01-17]

CODE REFACTORING:

  • Bumped package dependencies.

Version: 1.6.2 [2012-12-02]

CODE REFACTORING:

  • R CMD check no longer warns on global assignments.

  • Bumped up package dependencies.

Version: 1.6.1 [2012-06-30]

CODE REFACTORING:

  • Updated package dependencies.

Version: 1.6.0 [2012-06-07]

BUG FIXES:

  • 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]

NEW FEATURES:

  • It is now possible to specify the decompression method for readMat().

  • Now readMat() decompression error messages are more informative.

Version: 1.5.8 [2012-04-16]

CODE REFACTORING:

  • Package now only imports R.methodsS3.

Version: 1.5.7 [2012-04-13]

BUG FIXES:

  • 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]

BUG FIXES:

  • readMat(..., verbose=-111) gave an error on object 'zraw' not being found.

Version: 1.5.5 [2012-04-01]

SOFTWARE QUALITY:

  • 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.

DEPRECATED AND DEFUNCT:

  • 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]

CODE REFACTORING:

  • Removed all internal copies of 'base' functions that have .Internal() calls.

Version: 1.5.3 [2011-12-08]

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]

CODE REFACTORING:

  • Fixed an R CMD check NOTE that would show up in R v2.15.0 devel.

Version: 1.5.1 [2011-09-27]

CODE REFACTORING:

  • The version 1.5.0 that was submitted to CRAN did not include the adjustments for startup messages. Thus, resubmitting this one to CRAN.

  • Updated dependencies on R and packages.

Version: 1.5.0 [2011-09-24]

NEW FEATURES:

  • 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().

  • CLEANUP: Now using packageStartupMessage() instead of cat().

Version: 1.4.0 [2011-07-25]

CODE REFACTORING:

  • Added a namespace to the package, which will be more or less a requirement in the next major release of R.

  • 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().

DOCUMENTATION:

  • Added an example of verbose output to example(readMat).

Version: 1.3.7 [2011-02-01]

CODE REFACTORING:

  • Now using argument 'imaginary' (not partial 'imag') in calls to complex().

Version: 1.3.6 [2010-10-29]

NEW FEATURES:

  • Now writeMat() gives an error if duplicated object names are used, e.g. writeMat(..., A=1, B=2, A=3).

  • Now writeMat() gives an error, not a warning, if there are non-named objects.

BUG FIXES:

  • 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]

NEW FEATURES:

  • 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.

DOCUMENTATION:

  • Clarified in the help of writeMat() that it can only write 'uncompressed' MAT files.

Version: 1.3.4 [2010-10-26]

DOCUMENTATION:

  • Clarified and corrected some sentences in help(Matlab).

  • Added MATLAB 7.11.0.584 (R2010b) to the list of confirmed version that are compatible with R.matlab.

BUG FIXES:

  • 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 the report.

Version: 1.3.3 [2010-09-18]

BUG FIXES:

  • 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]

NEW FEATURES:

  • Now the MatlabServer script reports it's version when started.

DOCUMENTATION:

  • Removed some minor ambiguities in help(Matlab) and updated example(Matlab) with some more troubleshooting statements.

  • 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.

BUG FIXES:

  • 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]

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]

NEW FEATURES:

  • 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]

NEW FEATURES:

  • 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 the report.

Version: 1.2.5 [2009-08-25]

BUG FIXES:

  • 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 the report.

Version: 1.2.4 [2008-10-29]

NEW FEATURES:

  • 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.

BUG FIXES:

  • Arrays with more than two dimension would be written as vectors. Thanks Minho Chae for the report.

  • 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]

DOCUMENTATION:

  • Updated example(readMat) so that it gives no error if the optional 'Rcompression' package is not installed.

Version: 1.2.2 [2008-07-12]

NEW FEATURES:

  • 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).

CODE REFACTORING:

  • Removed internal debugging/asserting code.

  • Renamed the HISTORY file to NEWS.

Version: 1.2.1 [2008-05-08]

BUG FIXES:

  • 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]

NEW FEATURES:

  • Added support for reading compressed MAT files. It requires that the 'Rcompression' package (Omegahat.org) is available.

  • Added support for also returning sparse matrices according to the representations given by either the 'Matrix' or the 'SparseM' package.

  • Added simple UTF-* string support. Conversion should be accurate when the R installation supports iconv.

  • Added mat-files/StructWithSparseMatrix-v4.mat from JR.

  • 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]

NEW FEATURES:

  • 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]

CODE REFACTORING:

  • Update so that package passes R CMD check R v2.5.0.

  • Replaced Sys.putenv() with new Sys.setenv() (to be deprecated in R v2.5.0).

Version: 1.1.3 [2006-12-28]

NEW FEATURES:

  • Now open() throws an error if connection to MATLAB failed (before FALSE was returned).

  • Extended the accepted range of ports to [1023,66535].

DOCUMENTATION:

  • Added more details on available options in setOption() and how to avoid timeouts.

  • The example in help(Matlab) is now using default values for 'host' and 'port' making the example less confusing.

Version: 1.1.2 [2006-05-08]

BUG FIXES:

  • 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 the report.

Version: 1.1.1 [2006-01-21]

NEW FEATURES:

  • 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.

DOCUMENTATION:

  • 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]

CODE REFACTORING:

  • 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.

BUG FIXES:

  • Forgot to "implement" miSINGLE, i.e. to set 'knownTypes' and 'knownWhats' for this. Thanks to Craig Aumann for the report.

  • readMat() did not read 'complex' matrices in MAT v5 correctly. Thanks to Chris Sims for the report.

  • readMat() did not read 'text' matrices in MAT v4 correctly. Thanks to Chris Sims, Princeton University, for the patch.

Version: 1.0.3 [2005-05-26]

NEW FEATURES:

  • Added support for user-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 on this problem.

  • Added class Options. This will probably move to another package whenever it becomes stable and widely used.

Version: 1.0.2 [2005-05-03]

NEW FEATURES:

  • Now MATLAB struct's are read into an R structure.

CODE REFACTORING:

  • Replaces package directory misc/ with two new directories mat-files/ and externals/.

BUG FIXES:

  • 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.

Version: 1.0.1 [2005-04-08]

DOCUMENTATION:

  • Minor additions to help pages.

BUG FIXES:

  • readMat() failed to read some MATLAB struct's because of a parsing error.

  • 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.

  • The MatlabServer script did (indeed) not work with MATLAB v7; a wrong version was included. Thanks Patrick Drechsler, University of Wuerzburg for reporting the above two problems.

Version: 1.0 [2005-02-25]

SIGNFICANT CHANGES:

  • Moved to CRAN.

Version: 0.94 [2005-02-24]

NEW FEATURES:

  • 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.

DOCUMENTATION:

  • Added a Wishlist and an Acknowledgements section to "about".

  • Added more information on how to start the MATLAB server.

Version: 0.93 [2005-02-20]

DOCUMENTATION:

  • Updated the Matlab example to be more explicit about problems with Matlab$startServer() and MATLAB v7.

CODE REFACTORING:

  • Added autoload("hasVarArgs") to 000.R.

Version: 0.92 [2005-02-17]

CODE REFACTORING:

  • Package now passes R CMD check on R v2.1.0 devel without warnings.

  • Added appendVarArgs=TRUE to setMethodS3(), which specifies that '...' should be added, if missing.

  • Add argument '...' to all methods to make it even more consistent with any generic function. This is also done for a few methods in R base packages.

BUG FIXES:

  • readMat() would not read non-signed bytes correctly.

Version: 0.91 [2005-02-11]

DOCMENTATION:

  • Updated description of package. Preparing for moving to CRAN.

  • Added Rdoc comments to internal Verbose classes.

CODE REFACTORING:

  • Package passes R CMD check on R v2.1.0 devel too.

  • 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.

Version: 0.8 [2004-02-24]

NEW FEATURES:

  • Added a setVerbose() method to the Matlab class, which allows the user to get details at various levels of the MATLAB process.

  • Added support for reading sparse matrices. Sparse matrices are expanded to regular matrices, which means that some may be too large to be loaded.

BUG FIXES:

  • WORKAROUND: 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 workaround 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.

  • 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.

  • 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]

BUG FIXES:

  • 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]

NEW FEATURES:

  • 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.

  • writeMat() was created for consistency, but it does only support MAT v5.

  • 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]

CODE REFACTORING:

  • 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]

CODE REFACTORING:

  • 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 bit annoying.

BUG FIXES:

  • 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]

DOCUMENTATION:

  • Made all methods \keyword{internal}.

BUG FIXES:

  • readMAT() would not work because getBits() previously in package R.oo was removed. getBits() is now added as a local function inside readMAT().

Version: 0.2 [2002-10-23]

CODE REFACTORING:

  • Upgraded to make use of Rx.oo.

Version: 0.1 [2002-09-03]

NEW FEATURES:

  • Initial methods are readMAT() and writeMAT() for reading and writing MATLAB MAT file structures.

  • Initial class is Matlab, which provides static methods for communicating with the running MATLAB server.

  • Package created.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("R.matlab")

3.6.2 by Henrik Bengtsson, 2 months 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, SuperPCA, eemR, hNMF, lans2r, oXim, retistruct, scalpel, sisal.

Depended on by AnalyzeFMRI.

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


See at CRAN