http://blog.gmane.org/gmane.comp.lang.r.rcpp hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.lang.r.rcpp/3480 <pre>Hi all, Thanks for your help (Whit especially) on various things. After a fair bit of effort I got rccpbugs installed on my Mac 10.7 in R.app. Here's my setup: &gt; sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats grDevices utils datasets graphics methods base other attached packages: [1] rcppbugs_0.1.0 RcppArmadillo_0.3.0.2 Rcpp_0.9.10 inline_0.3.8 loaded via a namespace (and not attached): [1] compiler_2.14.1 tools_2.14.1 The basic steps: 1. Install dependencies install.packages("Rcpp") install.packages("inline") 2. (I updated Xcode to 3.2 and installed the Command Line Tools, I doubt the details of this matter though.) 3. The default compiler on Mac OS X 10.7 is gcc4.2. However, rcppbugs needs gcc4.6. I got gcc4.6 to install by following the directions here: http://solarianprogrammer.com/2011/12/01/comp</pre> Nick Matzke 2012-05-25T05:34:04 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3477 <pre>Hi, I've got Mac OS X 10.7, which still uses gcc4.2. I can install a separate copy of a newer gcc (e.g. 4.7), but is there a way to make Rcpp (and inline) use it while compiling? I suppose I could use a symbolic link to make gcc refer to gcc4.7 everywhere on my system, but that seems like an inflexible solution. Any help appreciated. Cheers! Nick </pre> Nick Matzke 2012-05-24T23:34:53 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3476 <pre> There had been a number of posts over the last few weeks (months?) where folks were struggling with getting Rcpp modules going based on the examples in the vignette. I just spent a few hours cleaning things up. The gist of it is -- this always worked, but I often forgot to point out that loading a module is different when you use inline to compile/load on the fly, and when you use a package; -- both uses were in fact documented in the vignette; -- both uses were in fact used in the unit tests too; but it was a little hard to get to. Now with the cleanup:: -- the unit test for Rcpp modules actually had three different modules which I commented a bit more, and also moved to the package created by Rcpp.package.skeleton("somePackageName, module=TRUE) to provide more direct examples -- I moved some things from the 'evaluate but do not show' mode of Sweave into full view, so the vignette should be a tad more helpful as well. So in short, "on the fly" and </pre> Dirk Eddelbuettel 2012-05-24T19:44:23 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3473 <pre>Rcpp List, Is there a recommended way to handle default arguments for constructors? I have a class that I have created and exposed through Rcpp Modules. I now found that I need to expose a tuning parameter and need to modify my constructors. The standard way would be to include just a default argument, but I didn't think that Rcpp could handle default arguments in constructors. Am I wrong? Any recommendations? Thanks, Andrew </pre> Andrew Redd 2012-05-24T18:34:20 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3469 <pre>Folks, May I thank the Rcpp community for providing such a useful package. For your records, may I let you know that the farming systems model APSIM (www.apsim.info) is using Rcpp/RInside as a wrapper around the R language; allowing snippets of R code to interact with apsim simulations. http://www.apsim.info/Wiki/RComponent.ashx has a brief outline. Source code is available from http://apsrunet.apsim.info/svn/apsim/trunk/Model/RLink/. There is particular nastiness involved on windows platforms as the model is built with MSVC, yet calls GCC code (ie Rcpp) via extern "C". Thanks again, Yours, PdeV </pre> Peter deVoil 2012-05-23T06:09:57 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3463 <pre>Greetings.  I'm trying to go through some of the examples in the notes from Dirk's Rcpp Masterclass of 28 April 2011.  (I didn't take the class.  I just found the notes on the Internet.  Please let me know if my use of them violates some law or protocol.  In case it makes any difference, I'm not making any money from this project.) I've run into a problem with the RInside "hello world" example.  I can not get it to compile on my system.  The first of the many error messages is:     undefined reference to `RInside::RInside(int, char const* const*, bool) I've appended the details.  I get the same error if I omit the reference to the c++0x standard.  What am I missing? Thanks, </pre> Michael Hannon 2012-05-22T07:29:43 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3462 <pre> Conrad released a new stable version 3.2.0 of Armadillo which I wrapped into RcppArmadillo 0.3.2.0. This version is now on CRAN. RcppArmadillo pre-releases do appear on R-Forge, and I did test the most recent pre-release on a number of CRAN packages depending on RcppArmadillo to ensure that everything still builds as usual. The NEWS entries since 0.3.0.3 are below, summarizing the changes for the new major release: 0.3.2.0 2012-05-21 o Upgraded to Armadillo release 3.2.0 "Creamfields" * faster eigen decomposition via "divide and conquer" algorithm * faster transpose of vectors and compound expressions * faster handling of diagonal views * faster handling of tiny fixed size vectors (≤ 4 elements) * added unique(), for finding unique elements of a matrix 0.3.1.94 2012-05-15 o Upgraded to Armadillo release 3.1.94 "v3.2 beta 2" * added unique(), for finding unique elements of a matrix * faster eigen decomposition via "divide and conquer"</pre> Dirk Eddelbuettel 2012-05-21T17:28:21 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3461 <pre>I have been running into yet another memory problem in testing the development version of lme4. After doing the usual valgrind, gctorture, gdb, etc. dance I found that the problem was originating in the destructor of an Eigen object that included some cholmod structures. The problem was that the particular place where it was failing is not a place where it should have gotten to. (It should only have called cholmod_free_factor and it was failing in cholmod_free_dense. Both of these are routines that are exposed through the funky R_GetCCallable function in RcppEigen/inst/include/RcppEigenStubs.h). The problem went away when I switched to g++. For the time being I would recommend caution if you choose to use clang++ to compile code linking to RcppEigen. </pre> Douglas Bates 2012-05-16T19:31:57 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3453 <pre>Dear Rcpp developers, ATM to define the Rcpp::Rostream I have to fix the iostream/Rostream.h header directly and add #include "Rstreambuf.h" before its declarations. Including "Rstreambuf.h" in my source file before "Rstreambuf.h" doesn't help, it seems the headers are processed in a way that Rostream declaration comes before Rstreambuf (due to RcppCommon.h that is included by Rstreambuf.h and not by Rostream.h). Is it possible to fix Rostream.h in the mainline or there's another proper way to include it? Thank you, Alexey _______________________________________________ Rcpp-devel mailing list Rcpp-devel-Z+qqJ2/841dDXCDGMXqaGq2UG9VpUWMKQH7oEaQurus&lt; at &gt;public.gmane.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</pre> Alexey Stukalov 2012-05-12T17:03:39 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3451 <pre>I am new to this list, so I hope this is the right place to ask this question. I am trying to translate the R vectorized loop below to C++ in order to speed up my calculations: Let: &gt; n1 [1] 1 1 2 2 2 3 3 4 4 4 5 5 5 5 6 6 6 7 7 8 8 8 9 9 &gt; n2 [1] 2 4 1 3 5 2 6 1 5 7 2 4 6 8 3 5 9 4 8 5 7 9 6 8 &gt; w1w1 [1] 0.2500000 0.2500000 0.1111111 0.1111111 0.1111111 0.2500000 0.2500000 [8] 0.1111111 0.1111111 0.1111111 0.0625000 0.0625000 0.0625000 0.0625000 [15] 0.1111111 0.1111111 0.1111111 0.2500000 0.2500000 0.1111111 0.1111111 [22] 0.1111111 0.2500000 0.2500000 My vectorized loop is: tWSWS.k &lt;- lapply(c(1:length(n1)), function(.n1){ lapply(c(1:length(n2)), function(.n2){ if(.n1!=.n2){ w1w1[n1==.n1 &amp; n2==.n2] }})}) result=sum(unlist(tWSWS.k)) Could you help me with this translation or at least point me out to some reference/example? Thanks! Nelson </pre> Nelson Villoria 2012-05-11T13:06:20 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3450 <pre> Conrad never rests, and has a first Armadillo test release 3.1.92 out en route to a new Armadillo version 3.2.0. I have wrapped this into RcppArmadillo 0.3.1.92. As the CRAN maintainers are trying to throttle uploads down a little, I will not push it to CRAN. But for those who are interested in trying the newest version, you should get it (once R-Forge builds tarballs from it, say tomorrow) via install.packages("RcppArmadillo", repos="http://R-Forge.R-project.org") and you can of course also always do an 'svn up' to fetch it. Cheers, Dirk </pre> Dirk Eddelbuettel 2012-05-10T13:45:32 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3434 <pre>Hi, Thank Dirk first for replying to my previous questions so fast. Another question: Suppose I have a function in CPP as void cppfun(Rcpp::List lst) { ...... } Then I would like to call this cppfun in R code as say cppfun(list(a=a, b=b, c=c, ...)), in which a, b, c could be of different types and their type might be different as this function gets called another time. So I would like to know the type of a, b, c in the CPP code. Could someone help me out or point to me some other approaches? Thanks. Best, Jiqiang _______________________________________________ Rcpp-devel mailing list Rcpp-devel-Z+qqJ2/841dDXCDGMXqaGq2UG9VpUWMKQH7oEaQurus&lt; at &gt;public.gmane.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</pre> Jiqiang Guo 2012-05-09T03:17:12 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3429 <pre>I have followed the Rcpp developer's recommendation that a package greatly simplifies using RCPP_MODULE wrappering. Unfortunately, I'm having difficulty building and checking even a simple package containing an Rcpp module. I have read previous posts on this topic but I did not find anything helpful. I must be overlooking something very simple, please help. The package check fails with this error: ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'mod', details: call: value[[3L]](cond) error: failed to load module mod from package mod no binding for "norm" The package skeleton was created with Rcpp.package.skeleton() to which I added a C++ source file and then edited files according to the 'Read-and-delete-me' file. Here are my build and check steps: $ R CMD build mod * checking for file `mod/DESCRIPTION' ... OK * preparing `mod': * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files * checking</pre> James Simone 2012-05-08T22:51:44 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3426 <pre>Hi all, I've been happily using the RcppEigen package for a couple of projects, but now I'm running into problems converting a matrix from R into an Eigen::MatrixXd. Converting an R matrix to an Eigen::Map&lt;Eigen::MatrixXd&gt; works fine, but I would like to (deep)copy the values from R to a C++ Eigen::MatrixXd object. From the definition for the Exporter for Eigen::Matrix&lt;T, Eigen::Dynamic, Eigen::Dynamic&gt; in RcppEigen/inst/include/RcppEigenWrap.h, it looks like Rcpp::as&lt;Eigen::MatrixXd&gt; could be used, but when compiling some example code (see below) I get an error (see below). Compiling the same code with an arma::mat or with Eigen::Map&lt;Eigen::MatrixXd&gt; does not result in any errors. Does anyone have an idea what is causing this? Many thanks in advance and best wishes, Jelmer R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=Engli</pre> Jelmer Ypma 2012-05-08T15:45:34 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3418 <pre>Dear list, I've noticed a small thing when compiling a .cpp file on windows. Following the Rcpp FAQ document I do C:\Documents\teaching\2012-ASC\presentations\callingC&gt;Rscript -e "Rcpp:::SHLIB('matprod5.cpp')" ------------------------------------ Sørens .Rprofile in c:/Documents ------------------------------------ Working directory is: C:/Documents/teaching/2012-ASC/presentations/callingC Calling .First() in .Rprofile exiting .First() g++ -m64 -shared -s -static-libgcc -o matprod5.dll tmp.def matprod5.o ------------------------------------ S▒rens .Rprofile in c:/Documents ------------------------- ----------- Working directory is: C:/Documents/teaching/2012-ASC/presentations/callingC Calling .First() in .Rprofile exiting .First() C:/programs/R/current/library/ Rcpp/lib/x64/libRcpp.aCalling .Last() in .Rprofile -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/programs/R/curren t/bin/x64 -lR g++.exe: error: S?rens: Invalid argument g++.ex</pre> Søren Højsgaard 2012-05-07T23:25:26 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3417 <pre>Hi, From http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-extending.pdf, we know that we could extend as. I would like to create an user-defined class instance from an SEXP (say a list in R). Where could I find more examples on this usage? Thanks, Jiqiang _______________________________________________ Rcpp-devel mailing list Rcpp-devel-Z+qqJ2/841dDXCDGMXqaGq2UG9VpUWMKQH7oEaQurus&lt; at &gt;public.gmane.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</pre> Jiqiang Guo 2012-05-07T22:23:39 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3414 <pre>I'm trying to build the qtdensity example which comes with RInside, using Qt Creator and the qtdensity.pro file included, but my build fails because g++ can't find libRInside.a. Running Rscript on command line shows that RInside:::LdFlags() does not return the full path, as it is doing for Rcpp, hence the error: -I/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/x86_64/libRcpp.a -I/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RInside/include /libRInside.a (RInside 0.2.6, OS 10.6.8). Have I missed something obvious here? The only thing I can think of is that it's an architecture issue, as there is no .../RInside/lib/x86_64/libRInside.a file. Thanks. jc (Melbourne) _______________________________________________ Rcpp-devel mailing list Rcpp-devel-Z+qqJ2/841dDXCDGMXqaGq2UG9VpUWMKQH7oEaQurus&lt; at &gt;public.gmane.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</pre> Jarny Choi 2012-05-07T13:26:39 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3408 <pre>Hi all, I'm a student at the University of Washington and my course project this spring involves rewriting the 'svmpath' R package into C++ using Rcpp and RccpArmadillo. Everything runs beautifully until I try to include the function below: vec solveKstar(mat Kstar){ vec onestar = ones&lt;vec&gt;(Kstar.n_cols); onestar[0]=0; vec solution; solution=solve(trimatu(Kstar),onestar); return solution; } If I run R CMD INSTALL on my package removing the call to 'solve' everything runs fine, but if I included the call to 'solve' then the R CMD INSTALL input is // all the typical output * installing to library ‘/net/home/aynlc3/Rlib’ * installing *source* package ‘aynSVMpath’ ... ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/net/home/aynlc3/Rlib/Rcpp/include" -I"/net/home/aynlc3/Rlib/RcppArmadillo/include" -fpic -O3 -pipe -g -c aynSVMpath.cpp -o aynSVMpath.o g++ -I/usr/share/R/include -DNDEBUG -I"/net/home/aynlc3/Rlib/Rcpp/include" -I"/net/home/aynlc3/Rlib/RcppArmadillo/include" -fpic -O3</pre> Ayn Leslie-Cook 2012-05-06T21:38:58 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3399 <pre>I was learning Rcpp and got the following problem in a basic example. I have searched online and knew someone have the same problem before, but did not find a good answer for this. Simply put, I am running the following script: rm -rf rcppapp1 R -q -e "library(Rcpp); Rcpp.package.skeleton(name = 'rcppapp1', module = TRUE);sessionInfo()" R CMD build rcppapp1 R CMD INSTALL rcppapp1 R -q -e "require(Rcpp);require('rcppapp1');m1&lt;-Module('yada', 'rcppapp1');m1\$hello()" But I could not run the hello function defined in the model yada. Here is the output: + rm -rf rcppapp1 + R -q -e 'library(Rcpp); Rcpp.package.skeleton(name = '\''rcppapp1'\'', module = TRUE);sessionInfo()' TRUE);sessionInfo() Creating directories ... Creating DESCRIPTION ... Creating NAMESPACE ... Creating Read-and-delete-me ... Saving functions and data ... Making help files ... Done. Further steps are described in './rcppapp1/Read-and-delete-me'. Adding Rcpp settings &gt;&gt; added RcppModules: yada &gt;&gt; added Depends: Rcpp &gt;&gt; added LinkingTo:</pre> Jiqiang Guo 2012-05-05T04:51:09 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3394 <pre>Hi, I am using a Makevar file for Rcpp package. It's from [ Rcpp.package.skeleton( ) ] command. I added something for GSL. GSL_CFLAGS = `gsl-config --cflags` GSL_LIBS = `gsl-config --libs` PKG_CXXFLAGS= `${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"` $(GSL_CFLAGS) PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(GSL_LIBS) Then, PKG_LIBS is working well. But PKG_CXXFLAGS is not working well. g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" * `/usr/lib64/R/bin/Rscript -e "Rcpp:::CxxFlags()"` `gsl-config --cflags` *-fpic -O3 -pipe -g -c rcpp_hello_world.cpp -o rcpp_hello_world.o g++ -shared -o RcppTest.so rcpp_hello_world.o *-L/usr/local/lib/R/site-library/Rcpp/lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib* *-L/usr/lib -lgsl -lgslcblas -lm *-L/usr/lib64/R/lib -lR Why are these different? Am I using wrong? Thank you, Seung _______________________________________________ Rcpp-devel mailing list Rcpp-devel-Z+qqJ2/841dDXCDGMXqaGq2UG9VpUWMK</pre> Seungki Kim 2012-05-03T14:52:58 http://comments.gmane.org/gmane.comp.lang.r.rcpp/3391 <pre>Doug, Apologies for my question, it's a little off topic from your original post (hence the modified subject). I've integrated Armadillo into the new mcmc packages I've been developing without giving much thought to Eigen. Unfortunately, the benchmarks page on the Armadillo site doesn't provide an Eigen benchmark: http://arma.sourceforge.net/speed.html Likewise, for the Eigen benchmark page: http://eigen.tuxfamily.org/index.php?title=Benchmark In your experience, do you find it to be faster than Armadillo? Have you done any benchmarking? If so, can you share the results (or the code)? Thanks, Whit On Wed, May 2, 2012 at 12:33 PM, Douglas Bates &lt;bates&lt; at &gt;stat.wisc.edu&gt; wrote: _______________________________________________ Rcpp-devel mailing list Rcpp-devel&lt; at &gt;lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</pre> Whit Armstrong 2012-05-03T12:20:32 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.rcpp