search for: pkg_libs

...allel. printf("Hello!\n"); } END_RCPP } As I am an absolute newbie with writing C++ extensions and have not much understanding of the Makevars file, 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 OpenMPTes...

Full_Name: Rick Sayre Version: 2.4.0 OS: Windows Submission from: (NULL) (138.72.27.164) PKG_LIBS works fine on *nix on windows, it seems to be ignored by the "SHLIB" script so, R CMD SHLIB blah properly uses PKG_CPPFLAGS and PKG_CFLAGS from Makevars, but PKG_LIBS is ignored

...nt at this point). src/Makevars is made such that the libraries are compiled individually to static libraries in their respective sub-directory, then these static libraries are copied to src/, and finally the static libraries are integrated into msa.so. The Makevars file looks as follows: PKG_LIBS=`${R_HOME}/bin${R_ARCH_BIN}/Rscript -e "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 ./libMuscl...

...LIBRARY_PATH is incorrect, but I don't seem to have it quite right yet. There are a few mentions of this problem in google, but thus far none of the "fixes" and fixed my problem. I've tried defining the LD_LIBRARY_PATH environment variable, and setting the PKG_CPPFLAGS, and PKG_LIBS environment variables as well. No luck so far. (initially would not compile, but specification of the PKG_CPPFLAGS, and PKG_LIBS got the compile to complete without errors). I still cannot load the library. My error message is: > library(RMySQL) Loading required package: DBI Error in dy...

...mple how the syntax is for passing the path of include files to: "If a package needs to specify additional directories for search- ing header les (`-I' options) or additional libraries for linking (`-l' and `-L' options), it should do this by setting the variables PKG_CPPFLAGS and PKG_LIBS in `src/Makevars'." But no examples. :-( src/Makevars. src/Makevars.in PKG_CPPFLAGS = @PKG_CPPFLAGS@ PKG_LIBS = @PKG_LIBS@ ? Eryk Eryk Witold Wolski Max Plank Institute fuer Molekulare Genetik Ihnestrasse 73 14195 Berlin Germany -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-...

...files? Is there a source for further information how to do it? "If a package needs to specify additional directories for search- ing header les (`-I' options) or additional libraries for linking (`-l' and `-L' options), it should do this by setting the variables PKG_CPPFLAGS and PKG_LIBS in `src/Makevars'." But no examples. :-( RMySQL/src/Makevars. doesnt exists. RMySQL/src/Makevars.in contains: PKG_CPPFLAGS = @PKG_CPPFLAGS@ PKG_LIBS = @PKG_LIBS@ ????? I added the path /prog/mysql/mysql/include \ to RMySQL/configure.in. But it doesnt work. After adding -Id:/prog/mys...

...ng to package some code to use with R and wanted to call Rscript from within the Makevars file (I am trying to automate the setting of the location of a third party library depending on what is available / the system the package is being installed on). If I just have a simple Makevars containing PKG_LIBS= -lnag_nag -L/fserver/nagprod/FL22/fll6a22df/lib the package is built without any errors, if I attempt to add a call to Rscript, for example (which I think is the way that "Writing R Extensions" recommends): R_SCRIPT_NAME=Rscript ifneq ($(R_HOME),) R_SCRIPT=$(R_HOME)/bin$(R_ARCH_BIN...

Following the recommendation of Prof. Ripley, I have created the Makevars file with the line: PKG_LIBS="-L/usr/lib/libm -lm -L/usr/local/lib/libgsl -lgsl -L/usr/local/lib /libgslcblas -lgslcblas" in the working directory. Now I have the code file Example3.c which computes the Bessel function value (the example is taken from the GSL reference book). I am running: R CMD SHLIB Example3.c and...

Dear R-list, I want to use shared library of gsl in R(2.15.1) on unix .I have a makefile such as CC = gcc CFLAGS = -fPIC -O2 PKG_LIBS -lgsl -lgslcblas -lm -lpthread ? OBJS_SPB = calc_spb.o k.o dk.o ddk.o ? ? calc_spb.so : $(OBJS_SPB) ? ????? $(CC) -shared -o calc_spb.so $(LIBS) $(OBJS_SPB) ? clean : ????? rm -f ../*.o *.o ? clean.so: ????? rm -f *.so ? I use R CMD SHLIB calc_spb.c in terminal window of unix and in my directory wa...

...--------- 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 something in lib) ------------------------------- ## Use the R_HOME indirection to support installations o...

...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) $(FLIBS)

...ql/mysql.h... yes Configuration error: could not find the MySQL installation include and/or library directories. Manually specify the location of the MySQL libraries and the header files and re-run R CMD INSTALL. INSTRUCTIONS: 1. Define and export the 2 shell variables PKG_CPPFLAGS and PKG_LIBS to include the directory for header files (*.h) and libraries, for example (using Bourne shell syntax): export PKG_CPPFLAGS="-I<MySQL-include-dir>" export PKG_LIBS="-L<MySQL-lib-dir> -lmysqlclient" Re-run the R INSTALL command: R CMD INSTAL...

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

...e/mysql/mysql.h... no Configuration error: could not find the MySQL installation include and/or library directories. Manually specify the location of the MySQL libraries and the header files and re-run R CMD INSTALL. INSTRUCTIONS: 1. Define and export the 2 shell variables PKG_CPPFLAGS and PKG_LIBS to include the directory for header files (*.h) and libraries, for example (using Bourne shell syntax): export PKG_CPPFLAGS="-I<MySQL-include-dir>" export PKG_LIBS="-L<MySQL-lib-dir> -lmysqlclient" Re-run the R INSTALL command: R CMD INSTALL RMy...

...X11_la_LDFLAGS) $(R_X11_la_OBJECTS) $(R_X11_la_LIBADD) $(LIBS) to $(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES) $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS) $(R_X11_la_LIBADD) $(LIBS) -L$(R_HOME)/bin -lR 2) I had the same link problem with ctest, so I changed PKG_LIBS = -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm to PKG_LIBS = -lg2c -lm -L/usr/lib/gcc-lib/i386-linux/2.95.4 -lm -L$(R_HOME)/bin -lR 3) Will all libraries that get loaded into R inside of python require this? If I try to load other 'recommended' packages that include C code I...

Hi All, I have already used gcc to creat a library, for example, it is called "test.a", which includes many c objects. How to link my main "a.c" function to this library when I used Rcmd SHLIB to complier my main c program? I tried "Rcmd SHLIB a.c test.a". It does not work this way. Does anyone have idea about this? Thanks, Xiaoping

...l autoload them if certain functions are called). 2) on page 3 of the R-exts document, it says to set PKG_* flags in 'Makeconf'; I think this should read 'src/Makevars' (this paragraph in general is pretty awkward reading). 3) I prefer PKG_LDFLAGS for the "-L" stuff and PKG_LIBS for the "-l" statements (currently the docs say to put it all in PKG_LIBS). 4) page 5 of R-exts gives an example of using autoconf to enable/disable R functions depending on whether or not a library is available; currently it suggests putting a test in the body of the function that is ex...

...sql/mysql.h... no Configuration error: could not find the MySQL installation include and/or library directories. Manually specify the location of the MySQL libraries and the header files and re-run R CMD INSTALL. INSTRUCTIONS: 1. Define and export the 2 shell variables PKG_CPPFLAGS and PKG_LIBS to include the directory for header files (*.h) and libraries, for example (using Bourne shell syntax): export PKG_CPPFLAGS="-I" export PKG_LIBS="-L -lmysqlclient" Re-run the R INSTALL command: R CMD INSTALL RMySQL_.tar.gz 2. Alternatively, you may pa...

...sql/mysql.h... no Configuration error: could not find the MySQL installation include and/or library directories. Manually specify the location of the MySQL libraries and the header files and re-run R CMD INSTALL. INSTRUCTIONS: 1. Define and export the 2 shell variables PKG_CPPFLAGS and PKG_LIBS to include the directory for header files (*.h) and libraries, for example (using Bourne shell syntax): export PKG_CPPFLAGS="-I<MySQL-include-dir>" export PKG_LIBS="-L<MySQL-lib-dir> -lmysqlclient" Re-run the R INSTALL command: R CMD INSTAL...