search for: pkg_cxxflag

..., _1 = 1); boost::thread t(thread); t.join(); return wrap(a); } ------------------------------- Makevars.win (try 1: try to find if there is a file called libboost_thread*) ------------------------------- ## Use the R_HOME indirection to support installations of multiple R version ## PKG_CXXFLAGS = `$(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()"` PKG_CPPFLAGS = -I${BOOSTLIB} PKG_LIBS = $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") ${BOOSTLIB}/lib/libboost_thread* ------------------------------- Makevars.win (try 2: try to find somethin...

Why is it that R places CFLAGS after PKG_CFLAGS and not before when compiling a package (e.g. through R CMD build pkg)? This can be problematic if, for instance, you want to use -O3, but -O2 is in R_HOME/etc/Makeconf. If -O2 (in CFLAGS) appears after -O3 (in PKG_CFLAGS), you are left with what you didn't want: -O2. In R-exts, it says that "Flags which are set in file etc/Makeconf

..., I am unsure what to write into it. Currently I have: ## Use the R_HOME indirection to support installations of multiple R version PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` KG_CFLAGS = $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) ## -- compiling for OpenMP PKG_CXXFLAGS=-fopenmp ## ## -- linking for OpenMP PKG_LIBS= -fopenmp -lgomp Obviously compilation fails with error: R CMD INSTALL OpenMPTest Symbol not found: __ZTIN4Rcpp19index_out_of_boundsE With standard setup of the above Makevars I get the Symbol not found: omp_set_num_threads Inline also does not wor...

...d, src/Makevars was wrong. I modified Makevars so that now looks like the below and the package now compiled and linked properly. CXX_STD = CXX11 PKG_LIBS += $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(shell ${R_HOME}/bin/Rscript -e "RcppParallel::RcppParallelLibs()") PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -I../inst/include Best, Sam On Thu, Oct 8, 2020 at 3:39 PM Dirk Eddelbuettel <edd at debian.org> wrote: > > Sam, > > PS It could of course also be something else: Is you src/Makevars for your > test package correct? Did you use `RcppArmadillo.pac...

...with some experience in using armadillo in R C++ extensions? My problem is the following: I programmed a function in a header looking like #include <armadillo> inline arma::vec foo(input) { ... do something return an arma::vec object } compiling this via R CMD INSTALL packagename (PKG_CXXFLAGS = -I/folder/of/armadillo and armadillo_bits in my package) I get the following error "error: expected initializer before 'foo' " The exact line and word is where inline arma::vec ends. Does anyone know what this error could be? Best Simon

I have been RTFM/doc/www, but I'm still lost. How does one tell R CMD INSTALL and R CMD check (both) that libraries are installed in non-usual places and so -I/APPS/include (or whatever) is necessary in CPPFLAGS and -L/APPS/lib (similarly) is necessary in LDFLAGS? I know I can hardwire them in pkg/src/Makevars, but this requires hand editing of that file by each installer (yuck!) rgentlem

I have been RTFM/doc/www, but I'm still lost. How does one tell R CMD INSTALL and R CMD check (both) that libraries are installed in non-usual places and so -I/APPS/include (or whatever) is necessary in CPPFLAGS and -L/APPS/lib (similarly) is necessary in LDFLAGS? I know I can hardwire them in pkg/src/Makevars, but this requires hand editing of that file by each installer (yuck!) rgentlem

Hello, I'm using a Makevars.in file and running my code through gdb. I understand i should turn of -O2, but R's makeconf overrides my settings /ln/meraki/custom/lib64/R/etc/Makeconf:112: warning: overriding commands for target `.cc.o' in Makevars.in .cc.o: g++ -g ${PKG_CXXFLAGS} ${PKG_LIBS} ${RINC} ${RLIB} -c $< -o $@ Thank you S.

...n_plus_one = xn*cos(angle)*radius; yn_plus_one = xn*sin(angle)*radius; angle += angle_increment; xn = grow*xn*(1-xn); x[i] = xn_plus_one; y[i] = yn_plus_one; } return List::create(Rcpp::Named("x") = x, Rcpp::Named("y") = y); } And I compile it like this: PKG_CXXFLAGS=$(Rscript -e 'Rcpp:::CxxFlags()') \ PKG_LIBS=$(Rscript -e 'Rcpp:::LdFlags()') \ R CMD SHLIB logistic_map.cpp without problems and I get a logistic_map.so file as expected. However in R: R> dyn.load("logistic_map.so") R> compute_values_cpp() Error in compute_values...

...stall 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()"` $(SHLIB_OPENMP_CXXFLAGS) CXX_STD = CXX11 and that of rrcov (which I m using for illustration's sake): PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS...

...efinitions in an extern "C" block. I still get the same error. Since I don't really understand what the extern "C" is supposed be doing here, I'm being pretty brainless about this. Note of course I'm compiling with a C++ compiler (g++) MAKEFLAGS='CXX=\ g++-3.1 PKG_CXXFLAGS=\ -Wall\ -pedantic\ -Werror\ -Wshadow ' R CMD SHLIB ms.cc -o ms.so Would someone be kind enough to tell me what the correct syntax is? It might also be helpful if someone could point to R code that uses compiled C++ code. Addendum: I looked at the file svm.h in the e1071 package source, and...

...e a shared library in Windows with customized level of optimization. Specifically, I would like to have "-O3 -funroll-loops" as flags when I run "R CMD SHLIB ***.cc" to speed the program for my simulations. I have read through the documentation and have tried adding the line PKG_CXXFLAGS = -O3 -funroll-loops in my Makevars in my package's src directory. However, this places the flags before the -O2 flag, thereby overriding it. I have also tried creating a config.site file in R_HOME/etc, but that seems to be ignored. I found a possible solution at http://tolstoy.newcastle.e...

...n undefined symbol in the *.so file. Is there something I can link in to resolve this problem? Is there another obvious solution? The system is FreeBSD 4.x-stable. The R version is 1.3.1. The gcc/g++ version is 2.95.3. I compile with R CMD INSTALL and my MAkevars file has the following lines: PKG_CXXFLAGS = -fPIC -I./ -I../../ PKG_CFLAGS = -fPIC -I./ -I../../ PKG_LIBS = -L/usr/local/lib The error I get when loading the library in R is: > library(rmetasim) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library "/usr/local/lib/R/library/rmetasi...

...e = xn*sin(angle)*radius; > angle += angle_increment; > xn = grow*xn*(1-xn); > x[i] = xn_plus_one; > y[i] = yn_plus_one; > } > return List::create(Rcpp::Named("x") = x, Rcpp::Named("y") = y); > } > > And I compile it like this: > PKG_CXXFLAGS=$(Rscript -e 'Rcpp:::CxxFlags()') \ > PKG_LIBS=$(Rscript -e 'Rcpp:::LdFlags()') \ > R CMD SHLIB logistic_map.cpp > without problems and I get a logistic_map.so file as expected. > > However in R: > R> dyn.load("logistic_map.so") > R> compute_va...

...ommit.? 3) I thought about cheating the system and add -O2? ? ?in the package CXXFLAGS, but Martin Morgan? ? ?recommends packages shouldn't mess and override system build defaults ? ?to mask and paper over the actual issue having a nasty abort()? ? ?lurking somewhere. ? ?But I couldn't add PKG_CXXFLAGS=-O2 in first place, since that? ? ?triggers the different WARNING that -O2 is not portable.? => Any help and input would be highly appreciated.? Thanks in advance,? yours, Steffen tmp.cpp by Martin Morgan (also in above linked mail thread) ------- #include <list> int foo(int argc, co...

...o speed things up we first install the binary install.packages("SeuratObject") # in this container via bspm/r2u as binary ## and then force a source installation (turning bspm off) _while Matrix is at 1.5.1_ if (requireNamespace("bspm", quietly=TRUE) bspm::disable() Sys.setenv(PKG_CXXFLAGS='-Wno-ignored-attributes') # Eigen compilation noise silencer install.packages('SeuratObject') ## we now remove the Matrix package version 1.5.1 we installed into /usr/local leaving 1.6.0 remove.packages("Matrix") packageVersion("Matrix") ## and we now run a...

Hi, I can not install packages from source which links to RcppArmadillo on Ubuntu 20.04 (after upgrading from 18.04). The following problem occurs: ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for 'myPackage' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object

...manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable compilation flags in Makevars ... WARNING Non-portable flags in variable ?PKG_CXXFLAGS?: -Wall -std=c++0x * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking examples ... OK * checking PDF version of manual ... OK WARNING: There were 2 warnings. NOTE: There were 2 notes. See ?/home/warmstrong/dvl/R.packages/rcppbugs.R...

...if (Sys.info()['sysname'] == 'Darwin') cat('-Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a') else cat('-Wl,--whole-archive ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -Wl,--no-whole-archive')"` PKG_CXXFLAGS=-I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" .PHONY: all mylibs all: $(SHLIB) $(SHLIB): mylibs mylibs: build_gc build_muscle build_clustalw build_clustalomega build_gc: make --file=m...

Hello, Does anyone know whether a Windows version of the Ratings package will be available? Thank you, Paul Prew CONFIDENTIALITY NOTICE: \ This e-mail communication an...{{dropped:11}}