mkl.h missing in installation on cluster with R 3.5.2 about rcppeigen HOT 4 CLOSED

Slowly. Your installation command echos DEIGEN_USE_MKL_ALL which we do not set. Breaking the line up we see

g++  -I"/appl/R/3.5.2-sl64/lib64/R/include" -DNDEBUG  \
  -I"/zhome/61/6/119429/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" \
  -DEIGEN_USE_MKL_ALL -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION \
  -I/usr/local/include  -I../inst/include -fpic  -I/appl/R/3.5.2-sl64/include -O2 -fomit-frame-pointer  \
  -c RcppEigen.cpp -o RcppEigen.o

If you need MKL I guess you (or your campus/cluster) needs to provide it. That has nothing to do with RcppEigen.

For comparison, on my box (with some local Debian/Ubuntu choices as well as ccache which I adore):

  ccache g++ -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"   \
  -I../inst/include -fpic  -g -O3 -Wall -pipe -DBOOST_NO_AUTO_PTR -Wno-sign-compare \
  -Wno-parentheses -Wno-maybe-uninitialized  -march=native -c RcppEigen.cpp -o RcppEigen.o

No RcppEigen as I can tell so I plan to close this. Ok?

from rcppeigen.

For future users' benefit, I might come back and update with more helpful information once I find it, but it's OK to close this.

from rcppeigen.

The problem was that the cluster was setup to use openBLAS, but another program I had run before was telling it to use MKL.

The solution was to edit the file ~/.R/Makevars to remove the part that was telling it to use MKL CPPFLAGS=-DEIGEN_USE_MKL_ALL -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I/usr/local/include.

I still get several warnings, but at least is seems to work.

from rcppeigen.

Yes, the warnings are an annoyannce. May make sense to collect a few compiler flags to make it better.

Anyway -- glad you have it working now as this really was a local issue.

from rcppeigen.