search for: rmatrix

...lse, null); System.out.println("Rengine created, waiting for R"); // the engine creates R is a new thread, so we should wait until it's // ready if (!re.waitForR()) { System.out.println("Cannot load R"); return null; } re.eval ("rmatrix <- matrix(data = NA, nrow = "+rows+", ncol ="+(columns-1)+", byrow = FALSE)");//,dimnames = )"); REXP rp= re.eval(hDr); //loop through the matrix and give the upgma_matrix the correct values for (int i = 0; i < rows-1; i++) { re.eval ("i&lt...

..., or call back into R, for fear of any assignment or allocation triggering an R event. R being single-threaded it cannot do this. My answer to this problem is to only use non-R data structures. That is what RcpParallel does in the actual parallel code portions in all examples -- types RVector and RMatrix do NOT connect back to R. There are several working examples. That is also what the OpenMP examples at the Rcpp Gallery do. Charles seems to be replying 'but I use XPtr' or 'I use XPtr on arma::mat or Eigen::Matrixxd' and seems to forget that these are proxy objects to SEXPs. XPtr...

...hat it means that R is single threaded? I am trying to understand what is actually going on inside R when users want to parallelize code. For example, using mclapply or foreach (with some backend) somehow allows users to benefit from multiple CPUs. Similarly there is the RcppParallel package for RMatrix/RVector objects. But none of these address the general XPtr objects in Rcpp. Some readers here may recognize my question on SO ( http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr) where I was curious about parallel calls to C++/Rcpp functions that return XPtr...

...lains much more of what I was looking for from the R side. Dirk, I'm sorry if I seem hung up on anything here but I am trying to understand the details. My reply about XPtr or XPtr on arma/Eigen was to confirm my understanding was correct, which it appears it was. I was not aware the RVector/RMatrix objects don't connect to R as I am just now familiarizing myself with the package, that explains more of my confusion. I will look at doing work within the compiled code as you have suggested. Regards, Charles On Thu, May 12, 2016 at 9:18 AM, Dirk Eddelbuettel <edd at debian.org> wrote:...

...7), skip_info = 0) Options in effect: --infile = chr22_1000G.gen --outfile = ./tmp841924 --skiprows = OFF --skipcols = 5 --cnrow = OFF --rncol = ON, using column 2 of 'chr22_1000G.gen' --transpose = ON --Rmatrix = OFF --nanString = NA Number of lines in source file is 120030 Number of words in source file is 11207 skiprows = 0 cnrow = 0 skipcols = 5 rncol = 2 Rmatrix = 0 numWords = 11207 Creating file with numRows = 120030 Creating file with numColumns = 11202 text2fvf finished. Data file size (...

...have missed a few since I didn't update the list for a while): Package: r-base r-base-core r-base-dev r-recommended r-cran-boot r-cran-cluster r-cran-class r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rmatrix r-cran-rpart r-cran-spatial r-cran-survival r-cran-tkrplot littler Pin: release o=Debian,a=unstable,l=Debian Pin-Priority: 900 Works like a charm... R 3.1.2 from SID. Hope this helps! (I can provide a more detailed source.list/preferences if necessary) Mathieu. > > Dirk > -- ~$ wh...

...edd at debian.org> Architecture: all Version: 2.6.1-1gutsy0 ... $ dpkg -s r-cran-matrix Package: r-cran-matrix Status: install ok installed Priority: optional Section: math Installed-Size: 3908 Maintainer: Ubuntu MOTU Developers <ubuntu-motu at lists.ubuntu.com> Architecture: i386 Source: rmatrix Version: 0.99875-2-1 ... > R.version _ platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 6.1 year 2007 month 11 day 26 svn rev 43537 language...

...=================================== INSTALLATION With an appropriate entry in /etc/apt/sources.list *(see below according to the branch of Debian used)*, the newest R release *including recommended packages* can be installed using a command sequence like SUPPORTED PACKAGES [Remove:] r-cran-rmatrix DEBIAN JESSIE (TESTING) As of end of January 2015, there is a new repository containing binaries for Jessie (current testing). This repository hosts all supported packages presented above, and is updated upon new R releases. To use R supported packages on Debian Jessie, simply add something l...

...ingle threaded? I am > trying to understand what is actually going on inside R when users want to > parallelize code. For example, using mclapply or foreach (with some > backend) somehow allows users to benefit from multiple CPUs. > > Similarly there is the RcppParallel package for RMatrix/RVector objects. > But none of these address the general XPtr objects in Rcpp. Some readers > here may recognize my question on SO ( > > http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr > ) > where I was curious about parallel calls to C++/R...

...appropriate entry in /etc/apt/sources.list *(see below according to >> the branch of Debian used)*, the newest R release *including recommended >> packages* can be installed using a command sequence like >> >> >> SUPPORTED PACKAGES >> >> [Remove:] r-cran-rmatrix >> >> >> DEBIAN JESSIE (TESTING) >> >> As of end of January 2015, there is a new repository containing binaries >> for Jessie (current testing). This repository hosts all supported packages >> presented above, and is updated upon new R releases. >> &g...

...didn't update the > list for a while): > > Package: r-base r-base-core r-base-dev r-recommended r-cran-boot > r-cran-cluster r-cran-class r-cran-codetools r-cran-foreign > r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv > r-cran-nlme r-cran-nnet r-cran-rmatrix r-cran-rpart r-cran-spatial > r-cran-survival r-cran-tkrplot littler > Pin: release o=Debian,a=unstable,l=Debian > Pin-Priority: 900 > > Works like a charm... R 3.1.2 from SID. > > Hope this helps! (I can provide a more detailed source.list/preferences if > necessary) >...

...m >> trying to understand what is actually going on inside R when users want to >> parallelize code. For example, using mclapply or foreach (with some >> backend) somehow allows users to benefit from multiple CPUs. >> >> Similarly there is the RcppParallel package for RMatrix/RVector objects. >> But none of these address the general XPtr objects in Rcpp. Some readers >> here may recognize my question on SO ( >> >> http://stackoverflow.com/questions/37167479/rcpp-parallelize-functions-that-return-xptr >> ) >> where I was curious about...

...LATION > > With an appropriate entry in /etc/apt/sources.list *(see below according to > the branch of Debian used)*, the newest R release *including recommended > packages* can be installed using a command sequence like > > > SUPPORTED PACKAGES > > [Remove:] r-cran-rmatrix > > > DEBIAN JESSIE (TESTING) > > As of end of January 2015, there is a new repository containing binaries > for Jessie (current testing). This repository hosts all supported packages > presented above, and is updated upon new R releases. > > To use R supported packag...

Hi Johannes, On 18 January 2015 at 20:47, Johannes Ranke wrote: | At the moment you are on your own with R 3.1.2 on jessie. The easiest safe bet in my opinion | would be to install from the Debian sources in unstable, i.e. add a deb-src entry for unstable | to your sources.list, do an apt-get build-dep r-base and then apt-get source --build r-base | and install the packages with dpkg. Ok. I

...pt/sources.list *(see below according to >>> the branch of Debian used)*, the newest R release *including recommended >>> packages* can be installed using a command sequence like >>> >>> >>> SUPPORTED PACKAGES >>> >>> [Remove:] r-cran-rmatrix >>> >>> >>> DEBIAN JESSIE (TESTING) >>> >>> As of end of January 2015, there is a new repository containing binaries >>> for Jessie (current testing). This repository hosts all supported packages >>> presented above, and is updated upon...

(I asked an earlier question on the rpy2 installation to the rpy2 list, the solution there was to edit the setup.py script, but this looks beyond what I can do unless someone tells me exactly what to modify). I have R 2.8.1 on 2 machines running ubuntu 8.04 (packages R-base and R-base-dev, among others, installed using Synaptic) and while the installation of rpy2 went fine on machine1, failed on