Writing `configure` file for an r package

I am writing an r package which provides a wrapper around the libSBML C library.

I am using the rcppgsl package as a reference, which looks for the location of header files and the library files for GNU Scientific Library GSL and uses that information to write the configure script and Makevars and Makevars.in. I am not building for Windows currently. On my machine (macOS), libsbml (SBML C library) is installed in usual locations, i.e.

header files are at - /usr/local/include/sbml

and library files at - /usr/local/lib. Indeed, if in my package Makevars file I use the following, I can build my package.

CXX=clang++
PKG_CPPFLAGS= -I/usr/local/include
PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) /usr/local/lib/libsbml-static.a

However, I want to learn how to use the configure script to find the library and use that information to build the package. The relevant portion of configure.ac from rcppgsl is

## Check for non-standard programs: gsl-config(1)
AC_PATH_PROG([GSL_CONFIG], [gsl-config])
## If gsl-config was found, let's use it
if test "${GSL_CONFIG}" != ""; then
    # Use gsl-config for header and linker arguments
    GSL_CFLAGS=`${GSL_CONFIG} --cflags`
    GSL_LIBS=`${GSL_CONFIG} --libs`
else
    AC_MSG_ERROR([gsl-config not found, is GSL installed?])
fi

I replaced GSL_CONFIG with LIB_SBML at relevant places, i.e., the entire configure.ac file I am using is pasted below (at the end).

However, I don't see configure, Makevars and Makevars.in being generated (which I see in rcppgsl). Any help here would be highly appreciated!

For the sake of completion, the output of ls -l | grep sbml (in usr/local/include) is

drwxrwxr-x   58 root      admin    1856 Aug  1  2016 sbml

and ls -l | grep sbml (in usr/local/lib) is

-rw-r--r--   1 root      wheel   7970584 Aug  2  2016 libsbml-static.a
-rwxr-xr-x   1 arcadmin  staff  10453624 Nov 25  2014 libsbml.5.11.0.dylib
-rwxr-xr-x   1 root      wheel   3813572 Aug  2  2016 libsbml.5.13.0.dylib
lrwxr-xr-x   1 root      wheel        20 Aug  1  2016 libsbml.5.dylib -> libsbml.5.13.0.dylib
-rw-r--r--   1 root      wheel  13907656 Feb 26  2015 libsbml.a
lrwxr-xr-x   1 arcadmin  staff        15 Mar 27  2015 libsbml.dylib -> libsbml.5.dylib
-rwxr-xr-x   1 root      wheel       828 Feb 26  2015 libsbml.la
-rwxrwxr-x   1 root      admin  13362732 Nov 25  2014 libsbmlj.jnilib

My configure.ac file --

## Process this file with autoconf to produce a configure script.
##
## Configure.ac for RcppSBML
##
## Copyright (C) 2010         Romain Francois and Dirk Eddelbuettel
## Copyright (C) 2014 - 2015  Dirk Eddelbuettel
##
## Licensed under GNU GPL 2 or later

# The version set here will propagate to other files from here
AC_INIT([Rcppsbml], 0.1.0)

# Checks for common programs using default macros
AC_PROG_CC

## Use gsl-config to find arguments for compiler and linker flags
##
## Check for non-standard programs: gsl-config(1)
AC_PATH_PROG([LIB_SBML], [libsbml])
## If gsl-config was found, let's use it
if test "${LIB_SBML}" != ""; then
    # Use gsl-config for header and linker arguments
    SBML_CFLAGS=`${LIB_SBML} --cflags`
    SBML_LIBS=`${LIB_SBML} --libs`
else
    AC_MSG_ERROR([libsbml not found, is SBML installed?])
fi

# Now substitute these variables in src/Makevars.in to create src/Makevars
AC_SUBST(LIB_SBML)
AC_SUBST(LIB_SBML)

AC_OUTPUT(src/Makevars)

Solution

Here a minimal setup:

Remove src/Makevars and create src/Makevars.in with content

PKG_CPPFLAGS= @SBML_INCLUDE@
PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @SBML_LIBS@

I am not setting CXX since you cannot change that in src/Makevars, c.f. Package build ignores Makevars flags.

Create a minimal configure.ac file:

AC_INIT([Rcppsbml], 0.1.0)

AC_LANG(C++)
AC_REQUIRE_CPP
AC_PROG_CXX

# default values
AC_SUBST([SMBL_INCLUDE], "-I/usr/local/include")
AC_SUBST([SMBL_LIBS], "/usr/local/lib/libsbml-static.a")

# allow for override
AC_ARG_WITH([smbl],
            AC_HELP_STRING([--with-smbl=PREFIX],
                           [path to where smbl is installed]),
            [
             SMBL_INCLUDE="-I${with_smbl}/include"
             SMBL_LIBS="${with_smbl}/lib/libsbml-static.a"
            ],
            [])

# create and report output
AC_CONFIG_FILES([src/Makevars])
AC_OUTPUT
echo
echo "Final src/Makevars"
cat src/Makevars

Call autoconf to create a configure file from your configure.ac template. You might want to check the script with ./configure and ./configure --with-smbl=/some/path.

Call

R CMD build ...
R CMD check [--install-args=--configure-args=--with-smbl=/some/path] ...
R CMD INSTALL [--configure-args=--with-smbl=/some/path]...

to build, check and install the package.

Possible extensions:

Allow for switching between static and dynamic linking.
Check that SMBL can be found in a usable state at the specified location.

I see three issues here:

The generation of configure from configure.ac is not automatic. You have to call autoconf.
Similarly, Makevars.in is not generated by the system. You have to provide it as template from which Makevars is generated by configure.
The GSL ships with gsl-config, other libraries make use of the general pkg-config. If your library does not support this, you can use the more traditional way to use default locations or those provided with --with-... arguments. For example in RcppArrayFire I use:
```
AC_SUBST([AF_INCLUDE], "")
AC_SUBST([AF_LIBS], "-laf")

AS_IF([test -e "${with_arrayfire}"],
        [
         AF_INCLUDE="-I${with_arrayfire}/include ${AF_INCLUDE}"
         AF_LIBS="-L${with_arrayfire}/lib ${AF_LIBS} -Wl,-rpath,${with_arrayfire}/lib"
        ])
```
If a directory is supplied as --with-arrayfire=/relevant/path, then appropriate sub directories are searched for headers and dynamic libraries.