Writing `configure` file for an r package

Question

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)

Aegina

Answer 1

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.

Noontide

Wow, thanks! There is so much here that I don't know (e.g., how to use autoconf while building a package, but thanks for the pointers. I will search for a step by step procedure, but would you be kind to add a little more details here? – Aegina

@ Ralf Stubner, Thanks!, I will give this a go and let you know the result. autoconf is very new to me but thanks for your detailed answer! – Aegina

Just want to add that there a very useful tutorial available about autoconf and configure for package developers at unconj.ca/blog/an-autoconf-primer-for-r-package-authors.html – Aegina