search for: rcppeigen

dear members, I am using R to model stock prices but a slow "for" loop has stifled my research. I am using Rcpp to speed up my "for" loop. I am also using RcppEigen to implement block operations on xts objects..... how do I use RcppEigen? If I just load it by: > require(RcppEigen) it is not recognising the .block method in C++. If I include it inside the cppFunction: > cppFunction(' include <RcppEigen.h> .....body') I get the fol...

RHEL 6 installed R version 3.2.3 from EPEL installed Start R and use the following command, but got warnings! install.packages("rstan", dependencies = TRUE, repos = "http://cran.r-project.org/") ... g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -L/usr/lib64/R/lib -lR /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status make: *** [RcppEigen.so] Error 1 ERROR: compilation failed for package 'RcppEigen...

...=============================downloaded 758 KB * installing *source* package ?TMB? ...** package ?TMB? successfully unpacked and MD5 sums checked** libsgcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/library/Matrix/include" -I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include" -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c external_metis.c -o external_metis.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/library/Matrix/include" -I"/home/drz/R/x86_64-pc-lin...

...crmda/tools/lib64/R/3.2/site-library/RcppArmadillo/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RcppArmadillo) * installing *source* package 'RcppEigen' ... ** package 'RcppEigen' successfully unpacked and MD5 sums checked ** libs g++ -I/tools/cluster/6.2/R/3.2.2_mkl/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.2/site-library/Rcpp/include" -I../inst/include -fpic -O3 -pipe -Wall -Wp,-D...

...crmda/tools/lib64/R/3.2/site-library/RcppArmadillo/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RcppArmadillo) * installing *source* package 'RcppEigen' ... ** package 'RcppEigen' successfully unpacked and MD5 sums checked ** libs g++ -I/tools/cluster/6.2/R/3.2.2_mkl/lib64/R/include -I/usr/local/include -I"/panfs/pfs.acf.ku.edu/crmda/tools/lib64/R/3.2/site-library/Rcpp/include" -I../inst/include -fpic -O3 -pipe -Wall -Wp,-D...

...; Warm regards. > > >> install.packages("openair", type = "source")Installing package into ?C:/R_Libs? > (as ?lib? is unspecified)Warning in install.packages : > dependencies ?lattice?, ?MASS? are not availablealso installing the > dependencies ?deldir?, ?RcppEigen?, ?cli?, ?glue?, ?lifecycle?, > ?pillar?, ?rlang?, ?tibble?, ?tidyselect?, ?vctrs?, ?png?, ?jpeg?, > ?interp?, ?timechange?, ?maps?, ?nlme?, ?Matrix?, ?cluster?, ?dplyr?, > ?hexbin?, ?latticeExtra?, ?lubridate?, ?mapproj?, ?mgcv?, ?purrr? > trying URL ' https://cran.rstudio.com/src/...

...ow if this is intentional?]; before we had the appropriate unloading hook, instead of segfaults we got errors about objects from the DLL not being found. The package has many complexities that might make it an especially tough case: it uses reference classes as well as making use of the Rcpp and RcppEigen packages ... I have tried running under valgrind and have seen what appear to be memory leaks but no memory access errors. The beginning and end of the valgrind output are appended below -- I can send the full output if anyone wants to see it ... I plan to continue to try to isolate the probl...

...> >> install.packages("openair", type = "source")Installing package into > ?C:/R_Libs? > > (as ?lib? is unspecified)Warning in install.packages : > > dependencies ?lattice?, ?MASS? are not availablealso installing the > > dependencies ?deldir?, ?RcppEigen?, ?cli?, ?glue?, ?lifecycle?, > > ?pillar?, ?rlang?, ?tibble?, ?tidyselect?, ?vctrs?, ?png?, ?jpeg?, > > ?interp?, ?timechange?, ?maps?, ?nlme?, ?Matrix?, ?cluster?, ?dplyr?, > > ?hexbin?, ?latticeExtra?, ?lubridate?, ?mapproj?, ?mgcv?, ?purrr? > > trying URL ' > http...

...dency (lme4). Here is the output from the installation: * installing *source* package ?lme4? ... ** package ?lme4? successfully unpacked and MD5 sums checked ** libs g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c external.cpp -o external.o In file included from external.cpp:8:0: predModul...

...nstall.packages("openair", type = "source")Installing package into >> ?C:/R_Libs? >> > (as ?lib? is unspecified)Warning in install.packages : >> > dependencies ?lattice?, ?MASS? are not availablealso installing the >> > dependencies ?deldir?, ?RcppEigen?, ?cli?, ?glue?, ?lifecycle?, >> > ?pillar?, ?rlang?, ?tibble?, ?tidyselect?, ?vctrs?, ?png?, ?jpeg?, >> > ?interp?, ?timechange?, ?maps?, ?nlme?, ?Matrix?, ?cluster?, ?dplyr?, >> > ?hexbin?, ?latticeExtra?, ?lubridate?, ?mapproj?, ?mgcv?, ?purrr? >> > trying URL...

...egister native routines for .C or .Fortran need to be re-installed for this version (unless installed with R-devel SVN revision r72375 or later). KernSmooth surely has .Fortran. Your spatial example had VR_frset failing, and that too is called by the old .C. A counter-example is eg my RcppEigen package -- I can load it and run example(fastLm) just fine as that uses .Call rather than .C or .Fortran. I think you are -- correct in that we need rebuilds -- but only for packages using .C and .Fortran calls to compiled This may be a use case for r-api-4. Or not as it doesn't break _all...

....1) But when I install my own package via CRAN it is compiled with the -o2 flag. My questions are what is causing my package's cpp code to be compiled in -o2 and how to fix this? Here is the content of the src/Makeconf file of my package (it is fairly standard I believe for a package using RcppEigen): PKG_CXXFLAGS = -I../inst/include -DEIGEN_DONT_PARALLELIZE $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CXXFLAGS) CXX_STD = CXX11 and that of rrcov (which I m using for illustration's sake): PKG_LIBS=$(LAPA...

---------- Forwarded message ---------- From: Akhil dua <akhil.dua.12@gmail.com> Date: Wed, Jul 4, 2012 at 10:33 AM Subject: To: r-help@r-project.org Hi everyone I have data on stock prices and market indices and I need to run a seperate regression of every stock on market so I want to write a "for loop" so that I wont have to write codes again and again to run the

...llery 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 just wrap the SEXP for external pointers; Arma's and Eigen's matrices are performant via RcppArmadillo and RcppEigen because we use R memory via proxies. All of that is 'too close to R' for comfort. So the short answer is: enter compiled code from R, set a mutex (either conceptually or explicitly), _copy_ your data in to plain C++ data structures and go to town in parallel via OpenMP and other multithr...

Pues parece que el problema si es de lme4, cuya versión 1.0-4 se publicó en septiembre de este año. En la página en cran del paquete pone "The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen "glue" " . El tema es que al utilizar esta versión junto con la librería boot, el tiempo de cálculo se incrementa bastante. Por suerte, en los repositorios de ubuntu aún viene la versión anterior (lme4_0.99999-2), en un paquete .deb . El 24 de octubre de 2013 13:06, José Luis Caña...

...d > R version 3.2.3 from EPEL installed > > Start R and use the following command, but got warnings! > > install.packages("rstan", dependencies = TRUE, repos = > "http://cran.r-project.org/") ... > g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o RcppEigen.so > g++ RcppEigen.o RcppExports.o fastLm.o -L/usr/lib64/R/lib -lRlapack > g++ -L/usr/lib64/R/lib -lRblas -lgfortran -lm -L/usr/lib64/R/lib -lR > /usr/bin/ld: cannot find -lgfortran > collect2: error: ld returned 1 exit status Install the gcc-gfortran package. > checking for curl...

...evel SVN revision r72375 or later). Yes, that is what Martin M?chler referred to in the answer to Bj?ran's call for help on r-help. > KernSmooth surely has .Fortran. Your spatial example had VR_frset failing, > and that too is called by the old .C. > > A counter-example is eg my RcppEigen package -- I can load it and run > example(fastLm) just fine as that uses .Call rather than .C or .Fortran. > > I think you are > > -- correct in that we need rebuilds > -- but only for packages using .C and .Fortran calls to compiled Yes. > This may be a use case for r-a...

...uld still be able to install car from within R, which you tried. On my raspi system using the unofficial Debian stretch image from https://wiki.debian.org/RaspberryPi3 I had to install ed (apt install ed) in order to get the dependency nloptr to compile. Now the compilation of the dependency RcppEigen is running (which seems to have failed or was interrupted on your system, judging by the error message you posted). Surely more than five minutes ago my raspi started to compile the file fastLm.cpp ... I will let you know if I succeed. But Dirk is right when he points out that the efficiency o...

Am Dienstag, 25. April 2017, 11:21:31 schrieb Dirk Eddelbuettel: > On 25 April 2017 at 16:11, Johannes Ranke wrote: > | This looks similar to what I got this morning when I tested my > | (unreleased) > | backport of R 3.4.0 to Debian jessie. My test was > | > | library(MASS) > | example(rlm) > | > | and there was an object that was not found. I am on a train on the way

...eems 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 just wrap the SEXP for external pointers; Arma's and Eigen's matrices > are performant via RcppArmadillo and RcppEigen because we use R memory via > proxies. All of that is 'too close to R' for comfort. > > So the short answer is: enter compiled code from R, set a mutex (either > conceptually or explicitly), _copy_ your data in to plain C++ data > structures > and go to town in parallel...