R package source install, no compiler

Question

I am trying to install some packages from source on a linux (RHEL) server. But whenever the package requires some C++ compilation it fails.

For example, I try to install Ckmeans.1d.dp package. If I call R CMD INSTALL Ckmeans.1.dp_4.2.1.tar.gz I get the following output (truncated) where you can see the compiler is omitted.

...* installing *source* package ‘Ckmeans.1d.dp’ ...
** libs
I/usr/include/R -DNDEBUG  -I/usr/local/include       -c Ckmeans.1d.dp.cpp -o Ckmeans.1d.dp.o
make: I/usr/include/R: Command not found
...
-shared -L/usr/local/lib64 -o Ckmeans.1d.dp.so Ckmeans.1d.dp.o Ckmeans.1d.dp_main.o dynamic_prog.o fill_SMAWK.o fill_log_linear.o fill_quadratic.o select_levels.o weighted_select_levels.o -L/usr/lib64/R/lib -lR
/bin/sh: line 2: -shared: command not found
make: *** [Ckmeans.1d.dp.so] Error 127
ERROR: compilation failed for package ‘Ckmeans.1d.dp’

I am currently stuck with a server that only has R 3.1.1 and I do not have admin privileges. The $Rhome/etc/Makeconf has CXX and CC defined. I have also verified g++ and gcc are installed.

What could be happening here?

Answer 1

Invariably an environment variable with an 'empty' value gets expanded. Maybe (just guessing here) the package would use C++11, so $(CXX11} -shared gets expanded and ... becomes -shared and an error is triggered.

Look at the R settings, eg via less $(R HOME)/etc/Makevars and see what it expects.

I think you can get by, if you must, installing gcc et al below, say, ~/bin . Some packages will require a compiler...