I am currently writing an R package packageFoo with RcppArmadillo. However, I have problems compiling my package in linux. I would be really glad if someone could help me. I do not know what I do wrong.
I only have a single cpp file with the following header:
#include <stdio.h>
#include <string>
#include <bitset>
#include <fstream>
#include <algorithm>
#include <iostream>
#include <cmath>
#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]
using namespace Rcpp;
When I do devtools::load_all() I get the following:
* installing *source* package ‘packageFoo’ ...
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/user/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.2/RcppArmadillo/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/user/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include" -I"/home/user/R/x86_64-pc-linux-gnu-library/3.2/RcppArmadillo/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c functions.cpp -o functions.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o packageFoo.so RcppExports.o functions.o -L/usr/lib/R/lib -lR
installing to /tmp/Rtmpvf8B08/devtools_install_63383fe5bd9a/packageFoo/libs
* DONE (packageFoo)
Loading required package: Matrix
Error in dyn.load(dllfile) :
unable to load shared object '/home/user/Documents/packageFoo/src/packageFoo.so':
/home/user/Documents/packageFoo/src/packageFoo.so: undefined symbol: dgesdd_
I googled around and found that dgesdd_ is part of lapack. Checking linking with ldd of packageFoo.so doesn't show any linked lapack libraries.
linux-vdso.so.1 => (0x00007ffc3615f000)
libR.so => /usr/lib/libR.so (0x00007f696e061000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f696dd5d000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f696da57000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f696d841000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f696d47c000)
libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f696d1ff000)
libreadline.so.6 => /lib/x86_64-linux-gnu/libreadline.so.6 (0x00007f696cfb9000)
libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f696cd7b000)
liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f696cb59000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f696c949000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f696c730000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f696c528000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f696c324000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f696c115000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f696bef7000)
/lib64/ld-linux-x86-64.so.2 (0x00007f696e831000)
libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f696bcce000)
My MakeVars file looks like this:
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
as described in the RcppArmadillo documentation. And running R CMD config LAPACK_LIBS returns -llapack
I am running R 3.2.5 with Rcpp_0.12.4, RcppArmadillo_0.6.700.3.0, and devtools_1.11.0
The issue is with the name of the Makevars file. Specifically, change the name of MakeVars to Makevars (Unix / Linux) or Makevars.win (Windows) and make sure it is placed within the src/ directory.