[Phylobase-commits] r726 - in pkg: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jan 30 22:47:13 CET 2010
Author: edd
Date: 2010-01-30 22:47:13 +0100 (Sat, 30 Jan 2010)
New Revision: 726
Modified:
pkg/configure
pkg/configure.in
pkg/src/NCLInterface.cpp
pkg/src/ReadWithNCL.cpp
Log:
fixes to the phylobase build to align with the new version of NCL:
-- src/{NCLInterface,ReadWithNCL}.cpp now use #include <ncl/ncl.h>
-- src/Makevars gets a -Iinclude from configure as the path is include/ncl/*
-- adjust configure accordingly
-- also suppress compile-time output from NCL
Modified: pkg/configure
===================================================================
--- pkg/configure 2010-01-28 15:35:40 UTC (rev 725)
+++ pkg/configure 2010-01-30 21:47:13 UTC (rev 726)
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.65 for phylobase 0.2.
+# Generated by GNU Autoconf 2.65 for phylobase 0.5.
#
#
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -548,8 +548,8 @@
# Identity of this package.
PACKAGE_NAME='phylobase'
PACKAGE_TARNAME='phylobase'
-PACKAGE_VERSION='0.2'
-PACKAGE_STRING='phylobase 0.2'
+PACKAGE_VERSION='0.5'
+PACKAGE_STRING='phylobase 0.5'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -1158,7 +1158,7 @@
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures phylobase 0.2 to adapt to many kinds of systems.
+\`configure' configures phylobase 0.5 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1219,7 +1219,7 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of phylobase 0.2:";;
+ short | recursive ) echo "Configuration of phylobase 0.5:";;
esac
cat <<\_ACEOF
@@ -1299,7 +1299,7 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-phylobase configure 0.2
+phylobase configure 0.5
generated by GNU Autoconf 2.65
Copyright (C) 2009 Free Software Foundation, Inc.
@@ -1391,7 +1391,7 @@
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by phylobase $as_me 0.2, which was
+It was created by phylobase $as_me 0.5, which was
generated by GNU Autoconf 2.65. Invocation command line was
$ $0 $@
@@ -1737,7 +1737,12 @@
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ ## package name, version
+## the CC and CFLAGS variables control configure tests, and they need to
+## be the same as what will be used when the package is built. There is
+## no need to place these flags in Makevars, and if no configure tests are
+## done they are not needed here (see "Writing R Extensions" manual).
: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "Could not determine R home directory"
@@ -1751,6 +1756,7 @@
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+ ## using C++
ac_ext=cpp
ac_cpp='$CXXCPP $CPPFLAGS'
@@ -2436,7 +2442,8 @@
-## With thanks to Kurt
+## Make sure we find R_HOME as several R instances could be installed
+## on the same machine -- with thanks to Kurt Hornik for the hint
: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
as_fn_error "Could not determine R_HOME." "$LINENO" 5
@@ -2494,26 +2501,21 @@
exit 1
fi
-CPPFLAGS="${CPPFLAGS} ${rcpp_cxxflags} -Iinclude/ncl"
+## configure include/load flags and copy sample source to inst/doc
+CPPFLAGS="${CPPFLAGS} ${rcpp_cxxflags} -Iinclude"
LDFLAGS="${LDFLAGS} ${rcpp_ldflags} -Llib/ncl -lncl"
-#echo "Building libRcpp.a in RcppSrc..."
-#cd src/RcppSrc
-#make RHOME=${R_HOME}
-#cd ../..
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: starting to build libncl.a in ncl" >&5
-$as_echo "$as_me: starting to build libncl.a in ncl" >&6;}
+{ $as_echo "$as_me:${as_lineno-$LINENO}: starting to build libncl.a in src/ncl" >&5
+$as_echo "$as_me: starting to build libncl.a in src/ncl" >&6;}
cd src/ncl
./configure --quiet --enable-static --disable-shared --prefix=`pwd`/..
-make
-make install
+make 2>&1 > /dev/null
+make install 2>&1 > /dev/null
cd ../..
-#ls -ltr src/
-{ $as_echo "$as_me:${as_lineno-$LINENO}: finished building libncl.a in ncl" >&5
-$as_echo "$as_me: finished building libncl.a in ncl" >&6;}
+{ $as_echo "$as_me:${as_lineno-$LINENO}: finished building libncl.a in src/ncl" >&5
+$as_echo "$as_me: finished building libncl.a in src/ncl" >&6;}
if test \! -d inst
then
@@ -3065,7 +3067,7 @@
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by phylobase $as_me 0.2, which was
+This file was extended by phylobase $as_me 0.5, which was
generated by GNU Autoconf 2.65. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -3118,7 +3120,7 @@
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-phylobase config.status 0.2
+phylobase config.status 0.5
configured by $0, generated by GNU Autoconf 2.65,
with options \\"\$ac_cs_config\\"
Modified: pkg/configure.in
===================================================================
--- pkg/configure.in 2010-01-28 15:35:40 UTC (rev 725)
+++ pkg/configure.in 2010-01-30 21:47:13 UTC (rev 726)
@@ -45,16 +45,16 @@
fi
## configure include/load flags and copy sample source to inst/doc
-AC_SUBST([CPPFLAGS],["${CPPFLAGS} ${rcpp_cxxflags} -Iinclude/ncl"])
+AC_SUBST([CPPFLAGS],["${CPPFLAGS} ${rcpp_cxxflags} -Iinclude"])
AC_SUBST([LDFLAGS],["${LDFLAGS} ${rcpp_ldflags} -Llib/ncl -lncl"])
-AC_MSG_NOTICE([starting to build libncl.a in ncl])
+AC_MSG_NOTICE([starting to build libncl.a in src/ncl])
cd src/ncl
./configure --quiet --enable-static --disable-shared --prefix=`pwd`/..
-make
-make install
+make 2>&1 > /dev/null
+make install 2>&1 > /dev/null
cd ../..
-AC_MSG_NOTICE([finished building libncl.a in ncl])
+AC_MSG_NOTICE([finished building libncl.a in src/ncl])
if test \! -d inst
then
Modified: pkg/src/NCLInterface.cpp
===================================================================
--- pkg/src/NCLInterface.cpp 2010-01-28 15:35:40 UTC (rev 725)
+++ pkg/src/NCLInterface.cpp 2010-01-30 21:47:13 UTC (rev 726)
@@ -21,7 +21,7 @@
// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
-#include "ncl.h"
+#include <ncl/ncl.h>
#include "NCLInterface.h"
#include <sstream>
#include <cassert>
Modified: pkg/src/ReadWithNCL.cpp
===================================================================
--- pkg/src/ReadWithNCL.cpp 2010-01-28 15:35:40 UTC (rev 725)
+++ pkg/src/ReadWithNCL.cpp 2010-01-30 21:47:13 UTC (rev 726)
@@ -34,7 +34,7 @@
// used here three times
#define Rf_length length
-#include "ncl.h"
+#include <ncl/ncl.h>
#include "NCLInterface.h"
using namespace std;
@@ -219,64 +219,4 @@
}
-/*
- * Sample function illustrates how to use the Rcpp R/C++ interface library.
- */
-/*
-RcppExport SEXP Rcpp_Example(SEXP params, SEXP nlist,
- SEXP numvec, SEXP nummat,
- SEXP df, SEXP datevec, SEXP stringvec,
- SEXP fnvec, SEXP fnlist) {
- SEXP rl=R_NilValue; // Use this when there is nothing to be returned.
- char* exceptionMesg=NULL;
-}
-*/
-
-
-/*
- * The following class definitions employ advanced features of the Rcpp
- * library and R, permitting the C++ programmer to call user-defined functions
- * on the R side. They should be skipped on first reading.
- */
-
-/*
- * Define a class that can be used to call an R function that expects a
- * real vector argument and returns a scalar. The R function is defined in
- * the example section of the documentation page for RcppExample (see
- * RcppExample.Rd).
- */
-class MyRVectorFunc : public RcppFunction {
-public:
- MyRVectorFunc(SEXP fn) : RcppFunction(fn) {}
-
- // This trivial function will use an R function to compute the
- // sum of the elements of v!
- double getSum(vector<double>& v) {
-
- // Turn vector into a SEXP that can be passed to R as an argument.
- setRVector(v);
-
- // Call the R function that was passed in as the paramter fn, with
- // the SEXP vector that was just set as its argument.
- SEXP result = vectorCall();
-
- // Assuming that the R function simply returns a real number we
- // pass it back to the C++ user as follows. If the R function returns
- // something more complicated transform result into a C++ object to
- // be returned, and clear the part of the protection stack due to
- // this object before returning (to prevent protection stack overflow).
- // Note that it is unsafe to do this if the returned result depends
- // on PROTECT-ed SEXP's. For example, result should not be
- // wrapped in a class like RcppParams where objects hold onto the
- // the PROTECT-ed SEXP that was used to construct them.
-
- double value = REAL(result)[0];
-
- // Safe now to clear the contribution of this function to the
- // protection stack.
- clearProtectionStack();
-
- return value;
- }
-};
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