separate R and utils build files

Author: Kieran Elmes

.Rbuildignore

@@ -0,0 +1 @@
+^utils$

DESCRIPTION

@@ -7,4 +7,5 @@ Description: Performs lasso regression on pairwise combinations of the input mat
 License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: true
+NeedsCompilation: yes
 RoxygenNote: 6.1.1

Makefile.am

@@ -1,3 +1,2 @@
-# Generated by roxygen2: do not edit by hand
-
-export()
+useDynLib("LassoTesting", .registration=TRUE)
+export(cyclic_lasso)

NAMESPACE

@@ -1,15 +1,16 @@
 #' @title Cyclic Lasso Function
 #'
+#' @name cyclic_lasso
 #' @description Performas a cyclic lasso
 #' @param X_filename, Y_filename, lambda, n, p
 #' @export
 #' @examples
 #' cyclic_lasso(xName = "X.csv", yName = "Y.csv", lambda = 20, n = 1000, p = 100)
+#' @useDynLib LassoTesting
 
-
-dyn.load("build/src/.libs/liblassoPackage.so.0")
 cyclic_lasso <- function(xName = "X.csv", yName = "Y.csv", lambda = 20, n = 1000, p = 100) {
-    Ret = .C("lasso", as.character(xName), as.character(yName), as.numeric(lambda), as.integer(n), as.integer(p))
+    #dyn.load(LassoTesting)
+    Ret = .Call(lasso_, as.character(xName), as.character(yName), as.numeric(lambda), as.integer(n), as.integer(p))
     #Ret = "test"
     return(Ret)
-}
+}

R/lasso.R

@@ -0,0 +1,5 @@
+#! /bin/sh
+
+rm -f config.* autom4te.cache src/Makevars src/config.h
+
+exit 0

cleanup

@@ -3,13 +3,17 @@
 
 AC_PREREQ([2.69])
 AC_INIT([FULL-PACKAGE-NAME], [VERSION], [BUG-REPORT-ADDRESS])
-AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_CONFIG_SRCDIR([config.h.in])
 AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_MACRO_DIRS([m4])
 m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
 LT_INIT
 
+AC_PATH_PROG([PKG_CONFIG], [pkg-config])
+if test -z "${PKG_CONFIG}"; then
+  AC_MSG_ERROR([cannot find pkg-config])
+fi
+
 # Checks for programs.
 AC_PROG_CC
 AC_PROG_CXX
@@ -18,15 +22,17 @@ AC_PROG_INSTALL
 AC_PROG_MKDIR_P
 
 # Checks for libraries.
-PKG_CHECK_MODULES(GLIB, glib-2.0)
-PKG_CHECK_MODULES(GSL, gsl)
-PKG_CHECK_MODULES(NCURSES, ncurses)
-PKG_CHECK_MODULES(R, libR)
 # FIXME: Replace `main' with a function in `-largeArrayDims':
 AC_CHECK_LIB([argeArrayDims], [main])
 # FIXME: Replace `main' with a function in `-lgomp':
 AC_CHECK_LIB([gomp], [main])
 
+PKG_CFLAGS=`"${PKG_CONFIG}" --cflags glib-2.0 ncurses libR gsl`
+PKG_LIBS=`"${PKG_CONFIG}" --libs glib-2.0 ncurses libR gsl`
+
+AC_SUBST(PKG_CFLAGS)
+AC_SUBST(PKG_LIBS)
+
 # Checks for header files.
 AC_CHECK_HEADERS([locale.h memory.h stdlib.h string.h sys/time.h unistd.h])
 
@@ -42,8 +48,5 @@ AC_FUNC_REALLOC
 AC_FUNC_STRTOD
 AC_CHECK_FUNCS([clock_gettime memset pow setlocale sqrt])
 
-AC_CONFIG_LINKS([./src/LassoTesting.so:./src/.libs/LassoTesting.so])
-
-AC_CONFIG_FILES([Makefile
-				 src/Makefile])
+AC_CONFIG_FILES([src/Makevars])
 AC_OUTPUT

configure.ac

@@ -6,3 +6,4 @@ add_project_arguments([
 
 subdir('src')
 subdir('tests')
+subdir('utils')