if test -z "${R_HOME}"; then
    echo "This command can be only executed via R CMD!"
    exit 1
fi

## pick up configure-time settings
. "${R_HOME}/etc${R_ARCH}/javaconf"

DYLIB_EXT=`${R_HOME}/bin/R CMD config DYLIB_EXT`
tools_classpath=${R_SHARE_DIR}/java

revision='$Rev$'
version=`set - ${revision}; echo ${2}`
version="R Java configurator: ${R_VERSION} (r${version})

Copyright (C) 2002-2013 The R Core Team.
This is free software; see the GNU General Public License version 2
or later for copying conditions.  There is NO warranty."

usage="
Usage: R CMD javareconf [options]

Detect current Java setup and update the corresponding configuration in R.

Options:
  -h, --help     print this help message and exit
  -v, --version  print version info and exit
  -n, --dry-run  perform Java detection, but don't touch any
                 configuration files
  -e <prog>      same as -n but exports all detected variables
                 and runs <prog>. If -e is the last argument
                 or <prog> is '' then a shell is used instead
  xxx=yyy        evaluate the corresponding expression
                 (e.g. JAVA_HOME=/usr/lib/java)

Environment variables that can be used to influence the detection:
  JAVA           path to a Java interpreter executable
                 By default first 'java' command found on the PATH
                 is taken (unless JAVA_HOME is also specified).
  JAVA_HOME      home of the Java environment. If not specified,
                 it will be detected automatically from the Java
                 interpreter.
  JAVAC          path to a Java compiler
  JAVAH          path to a Java header/stub generator
  JAR            path to a Java archive tool

The following variables should be used with extreme caution. They
must all match, so use only if you have a very special setup that
javareconf cannot detect automatically:
  JAVA_LD_LIBRARY_PATH library path necessary at run-time
  JAVA_CPPFLAGS  C preprocessor flags necessary to compile JNI programs
  JAVA_LIBS      libraries (as linker flags) necessary to compile
                 JNI programs

Report bugs at bugs.r-project.org ."


dry_run=no
export_vars=no
while test -n "${1}"; do
    case ${1} in
	-help | --help | -h) echo "${usage}"; exit 0 ;;
	-v | --version) echo "${version}"; exit 0 ;;
	-n | --dry-run) dry_run=yes ;;
	-e) dry_run=yes; export_vars=yes; run_prog="${2}"; if test "$#" != 1; then shift; fi ;;
	*=*) eval ${1} ;;
    esac
    shift
done

## find java compiler binaries
if test -z "${JAVA_HOME}" ; then
    JAVA_PATH=${PATH}
else
    if test ! -d "${JAVA_HOME}"; then
	echo "*** JAVA_HOME is not a valid path, ignoring"
	JAVA_HOME=
	JAVA_PATH=${PATH}
    else
	## try jre/bin first just in case we don't have full JDK
	JAVA_PATH=${JAVA_HOME}:${JAVA_HOME}/jre/bin:${JAVA_HOME}/bin:${JAVA_HOME}/../bin:${PATH}
    fi
fi
## if 'java' is not on the PATH or JAVA_HOME, add some guesses as of
## where java could live
JAVA_PATH=${JAVA_PATH}:/usr/java/bin:/usr/jdk/bin:/usr/lib/java/bin:/usr/lib/jdk/bin:/usr/local/java/bin:/usr/local/jdk/bin:/usr/local/lib/java/bin:/usr/local/lib/jdk/bin

if test -z "$JAVA"; then
    save_IFS=$IFS; IFS=:
    for dir in ${JAVA_PATH}; do
	if test -f "$dir/java"; then
	    JAVA="$dir/java"
	    break
	fi
    done
    IFS=${save_IFS}
fi

if test -z "$JAVA"; then
    echo "~*** Cannot find any Java interpreter~*** Please make sure 'java' is on your PATH or set JAVA_HOME correspondingly"|${SED-sed} -e 'y/~/\n/' >&2
    exit 1
fi

echo "Java interpreter : $JAVA"
jires=`$JAVA -classpath ${tools_classpath} getsp -test`
if test "$jires" != "Test1234OK"; then
    echo "$jires"
    echo "~*** Java interpreter doesn't work properly.~"|${SED-sed} -e 'y/~/\n/' >&2
    exit 1
fi

if test -z "${JAVA_HOME}"; then
    JAVA_HOME=`$JAVA -classpath ${tools_classpath} getsp java.home`
fi

if test -z "${JAVA_HOME}"; then
    echo "~*** Cannot find Java environemnt.~*** Please set JAVA_HOME correspondingly.~"|${SED-sed} -e 'y/~/\n/' >&2
    exit 1
fi

echo "Java version     : `$JAVA -classpath ${tools_classpath} getsp java.version 2>/dev/null`"
echo "Java home path   : ${JAVA_HOME}"

# optional parts - compiler, javah and jar
if test -z "$JAVAC"; then
    save_IFS=$IFS; IFS=:
    for dir in ${JAVA_PATH}; do
	if test -f "$dir/javac"; then
	    JAVAC="$dir/javac"
	    break
	fi
    done
    IFS=${save_IFS}
fi

: ${TMPDIR=/tmp}
{ tempdir=`(mktemp -d -q "${TMPDIR}/Rjavareconf.XXXXXX") 2>/dev/null` \
	&& test -n "${tempdir}" && test -d "${tempdir}" ; } ||
{ test -n "${RANDOM}" && tempdir=${TMPDIR}/Rjavareconf.$$-${RANDOM} \
	&& (mkdir "${tempdir}") ; } ||
{ tempdir=${TMPDIR}/Rjavareconf.$$-`date +%m%d%H%M%S` \
	&& (mkdir "${tempdir}"); } ||
{ tempdir=${TMPDIR}/Rjavareconf.$$ && (mkdir "${tempdir}") ; } ||
    (error "cannot create temporary directory" && exit 1)

# test functionality of the compiler
javac_works='not present'
if test -n "$JAVAC"; then
    javac_works='not functional'
    echo "public class A { }" > "${tempdir}/A.java"
    if test -f "${tempdir}/A.java"; then
	if "${JAVAC}" "${tempdir}/A.java" >/dev/null; then
           if test -f "${tempdir}/A.class"; then
		javac_works=yes
	    fi
	fi
    fi
fi
if test "${javac_works}" = yes; then
    echo "Java compiler    : ${JAVAC}"
else
    echo "Java compiler    : ${javac_works}"
fi

if test -z "$JAVAH"; then
    save_IFS=$IFS; IFS=:
    for dir in ${JAVA_PATH}; do
	if test -f "$dir/javah"; then
	    JAVAH="$dir/javah"
	    break
	fi
    done
    IFS=${save_IFS}
fi
echo "Java headers gen.: ${JAVAH}"

if test -z "$JAR"; then
    save_IFS=$IFS; IFS=:
    for dir in ${JAVA_PATH}; do
	if test -f "$dir/jar"; then
	    JAR="$dir/jar"
	    break
	fi
    done
    IFS=${save_IFS}
fi
echo "Java archive tool: ${JAR}"

: ${JAVA_LIBS=~autodetect~}
: ${JAVA_CPPFLAGS=~autodetect~}
: ${JAVA_LD_LIBRARY_PATH=~autodetect~}
custom_JAVA_LIBS="${JAVA_LIBS}"
custom_JAVA_CPPFLAGS="${JAVA_CPPFLAGS}"
custom_JAVA_LD_LIBRARY_PATH="${JAVA_LD_LIBRARY_PATH}"


# sys-dependent tweaks to JNI flags
hostos=`uname 2>/dev/null`
if test "${hostos}" = "Darwin"; then
     pref=`echo "${JAVA_HOME}" | grep "/Home$"`
     if test "${pref}" = "${JAVA_HOME}"; then 
       echo "System Java on OS X"
       JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers"
       JAVA_LIBS="-framework JavaVM"
       JAVA_LD_LIBRARY_PATH=
	has_libjvm=unknown
    else
       echo "Non-system Java on OS X"
    fi
fi
## we now look for a path to put in R_LD_LIBRARY_PATH which will
## enable libjvm to be found at run time.  This should not be needed,
## but it seems that libjvm is often not in the ld.so cache.
if test "${JAVA_LIBS}" = "~autodetect~"; then
	## we need to reset LD_LIBRARY_PATH, because Java automatically
	## adds all LD_LIBRARY_PATH to Java path
	save_LDLP=${LD_LIBRARY_PATH}
	LD_LIBRARY_PATH=
	export LD_LIBRARY_PATH
	# remove trailing/leading : (if any)
	java_library_path=`"$JAVA" -classpath "${tools_classpath}" getsp java.library.path| ${SED-sed} -e 's/:$//' -e 's/^://'`
	## see if libjvm is on this path: it is not for recent Oracle Java
	has_libjvm=no
	save_IFS=$IFS; IFS=:
	for dir in ${java_library_path}; do
	    if test -f "$dir/libjvm${DYLIB_EXT}"; then
		has_libjvm=yes
		java_library_path="${dir}"
		break
	    fi
	done
	# Then try some heuristics using sun.boot.library.path
	if test ${has_libjvm} = no; then
	    boot_path=`"$JAVA" -classpath "${tools_classpath}" getsp sun.boot.library.path| ${SED-sed} -e 's/:$//' -e 's/^://'`
	    if test -n "${boot_path}"; then
		for dir in "${boot_path}" "${boot_path}/client" "${boot_path}/server"; do
		    if test -f "$dir/libjvm${DYLIB_EXT}"; then
			has_libjvm=yes
			java_library_path="${dir}"
			break
		    fi
		done
	    fi
	fi	
	IFS=${save_IFS}
	# replace occurrences of JAVA_HOME with $(JAVA_HOME)
	# If JAVA_HOME was a link, it will be the canonical path we
	# want to replace.  We need realpath to determine what that is.
	if test "@REALPATH@" != "false"; then
             java_home=`@REALPATH@ "${JAVA_HOME}"`
	else
       	    java_home="${JAVA_HOME}"
	fi
	JAVA_LD_LIBRARY_PATH=`echo "${java_library_path}" | ${SED-sed} -e" s:${java_home}:\$\(JAVA_HOME\):g"`

	LD_LIBRARY_PATH=${save_LDLP}
	export LD_LIBRARY_PATH
	# build JAVA_LIBS from the detected path
	JAVA_LIBS=`echo ${JAVA_LD_LIBRARY_PATH}|${SED-sed} -e 's|:| -L|g'`
	if test -n "${JAVA_LIBS}"; then JAVA_LIBS="-L${JAVA_LIBS}"; fi
	JAVA_LIBS="${JAVA_LIBS} -ljvm"
	# create shell-version to be used in scripts
	JAVA_LD_LIBRARY_PATH_SH=`echo ${JAVA_LD_LIBRARY_PATH}|${SED-sed} -e 's:$(JAVA_HOME):\$\{JAVA_HOME\}:g'`

        ## includes consist of two parts - jni.h and machine-dependent jni_md.h
        jinc=''
	JAVA_CPPFLAGS=''
        for pinc in include ../include jre/include; do
          if test -f "${JAVA_HOME}/${pinc}/jni.h"; then jinc="${JAVA_HOME}/${pinc}"; break; fi
        done
        ## only if we get jni.h we can try to find jni_md.h
        if test -n "${jinc}"; then
           JAVA_CPPFLAGS="-I${jinc}"
           jmdinc=''
           jmdirs=''
	   ## we are not in configure, so we need to find the OS from R
	   host_os=`echo 'cat(R.version$os)'|${R_HOME}/bin/R --vanilla --slave 2>/dev/null`
           ## put the most probable locations for each system in the first place
           case "${host_os}" in
             darwin*)  jmdirs=darwin;;
             linux*)   jmdirs=linux;;
             bsdi*)    jmdirs=bsdos;;
             osf*)     jmdirs=alpha;;
             solaris*) jmdirs=solaris;;
             freebsd*) jmdirs=freebsd; add_java_libs='-lpthread';;
           esac
	   ## in case host_os detection failed, add all candidates
	   if test -z "${jmdirs}"; then jmdirs='linux solaris freebsd alpha bsdos'; fi
           ## prepend . and append less-likely ones
           jmdirs=". ${jmdirs} genunix ppc x86 iris hp-ux aix win32 cygwin openbsd"
           for pimd in ${jmdirs}; do
             if test -f "${jinc}/${pimd}/jni_md.h"; then jmdinc="${jinc}/${pimd}"; break; fi
           done
           if test -z "${jmdinc}"; then
             # ultima-ratio: use find and pray that it works
             jmdinc=`find "${jinc}/" -name jni_md.h 2> /dev/null |head -n 1 2>/dev/null`
             if test -n "${jmdinc}"; then jmdinc=`dirname "${jmdinc}"`; fi
           fi
           if test -n "${jmdinc}"; then
             if test "${jmdinc}" != "${jinc}/."; then
               JAVA_CPPFLAGS="${JAVA_CPPFLAGS} -I${jmdinc}"
             fi
           fi
	   JAVA_CPPFLAGS=`echo ${JAVA_CPPFLAGS} | ${SED-sed} -e s:${JAVA_HOME}:\$\(JAVA_HOME\):g`
        fi
fi

if test -n "${add_java_libs}"; then JAVA_LIBS="${JAVA_LIBS} ${add_java_libs}"; fi

## honor user overrides
acx_custom_java_libs=no
if test "${custom_JAVA_LIBS}" != '~autodetect~'; then
  JAVA_LIBS="${custom_JAVA_LIBS}"
  JAVA_LIBS0=`echo ${JAVA_LIBS} | ${SED-sed} -e s:${JAVA_HOME}:\$\(JAVA_HOME\):g`
  acx_custom_java_libs=yes
fi
if test "${custom_JAVA_CPPFLAGS}" != '~autodetect~'; then
  JAVA_CPPFLAGS="${custom_JAVA_CPPFLAGS}"
fi
if test "${custom_JAVA_LD_LIBRARY_PATH}" != '~autodetect~'; then
  JAVA_LD_LIBRARY_PATH="${custom_JAVA_LD_LIBRARY_PATH}"
  JAVA_LD_LIBRARY_PATH_SH=`echo ${JAVA_LD_LIBRARY_PATH}|${SED-sed} -e 's:$(JAVA_HOME):\$\{JAVA_HOME\}:g'`
fi

## Do cpmpile test in the temporary dir
wd=${PWD}
cd "${tempdir}"

echo
echo "trying to compile and link a JNI progam "
echo "detected JNI cpp flags    : ${JAVA_CPPFLAGS}"
echo "detected JNI linker flags : ${JAVA_LIBS}"

cat <<_ACEOF >conftest.c
#include <jni.h>

int main(void) {
    JNI_CreateJavaVM(0, 0, 0);
    return 0;
}
_ACEOF

JAVA_CPPFLAGS1=`echo ${JAVA_CPPFLAGS}|${SED-sed} -e 's:$(JAVA_HOME):'"${JAVA_HOME}:g"`
JAVA_LIBS1=`echo ${JAVA_LIBS}|${SED-sed} -e 's:$(JAVA_HOME):'"${JAVA_HOME}:g"`
cat <<_ACEOF >Makevars
PKG_CPPFLAGS = ${JAVA_CPPFLAGS1}
PKG_LIBS = ${JAVA_LIBS1}
_ACEOF

## in case e.g. -k was passed in the environment
export MAKEFLAGS=
${R_HOME}/bin/R CMD SHLIB conftest.c
ac_status=$?

if test $ac_status != 0; then
  echo "Unable to compile a JNI program"
  JAVA_LD_LIBRARY_PATH=
  JAVA_LIBS=
  JAVA_CPPFLAGS=
fi

rm -f conftest.c conftest.o conftest.so Makevars
cd ${wd}
rm -rf "${tempdir}"


echo ""

if test "${export_vars}" = yes; then
    ## we have to re-substitute $(JAVA_HOME), 
    ## otherwise it will be replaced by R's Makeconf setting
    ## which is highly likely different and thus not intended
    JAVA_LD_LIBRARY_PATH=`echo ${JAVA_LD_LIBRARY_PATH}|${SED-sed} -e 's:$(JAVA_HOME):'"${JAVA_HOME}:g"`
    JAVA_CPPFLAGS=`echo ${JAVA_CPPFLAGS}|${SED-sed} -e 's:$(JAVA_HOME):'"${JAVA_HOME}:g"`
    JAVA_LIBS=`echo ${JAVA_LIBS}|${SED-sed} -e 's:$(JAVA_HOME):'"${JAVA_HOME}:g"`

    export JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
    echo "The following Java variables have been exported:"
    echo "JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH"
    test -z "${run_prog}" && test -n "${SHELL}" && run_prog="${SHELL}"
    test -z "${run_prog}" && run_prog=/bin/sh
    echo "Running: ${run_prog}"
    ${run_prog}
    exit 0
fi

echo ""
echo "JAVA_HOME        : ${JAVA_HOME}"
echo "Java library path: ${JAVA_LD_LIBRARY_PATH}"
echo "JNI cpp flags    : ${JAVA_CPPFLAGS}"
echo "JNI linker flags : ${JAVA_LIBS}"

test "${dry_run}" = yes && exit 0

echo "Updating Java configuration in ${R_HOME}"

## We update both the base and arch-specific versions as etc/Makefile
## copies the first to the second (only the second is used).
if test -n "${R_ARCH}"; then
  files="${R_HOME}/etc/Makeconf ${R_HOME}/etc/ldpaths ${R_HOME}/etc${R_ARCH}/Makeconf ${R_HOME}/etc${R_ARCH}/ldpaths"
else
  files="${R_HOME}/etc/Makeconf ${R_HOME}/etc/ldpaths"
fi
for file in $files; do
    ${SED-sed} -e "s|JAVA =.\{0,\}|JAVA = $JAVA|" -e "s|JAVA_HOME =.\{0,\}|JAVA_HOME = ${JAVA_HOME}|" -e "s|: \${JAVA_HOME=.\{1,\}|: \${JAVA_HOME=${JAVA_HOME}}|" -e "s|: \${R_JAVA_LD_LIBRARY_PATH=.\{1,\}|: \${R_JAVA_LD_LIBRARY_PATH=${JAVA_LD_LIBRARY_PATH_SH}}|" -e "s|JAVA_LIBS =.\{0,\}|JAVA_LIBS = ${JAVA_LIBS}|g" -e "s|JAVA_LD_LIBRARY_PATH =.\{0,\}|JAVA_LD_LIBRARY_PATH = ${JAVA_LD_LIBRARY_PATH}|" -e "s|JAVAC =.\{0,\}|JAVAC = $JAVAC|" -e "s|JAVAH =.\{0,\}|JAVAH = $JAVAH|" -e "s|JAR =.\{0,\}|JAR = $JAR|" -e "s|JAVA_CPPFLAGS =.\{0,\}|JAVA_CPPFLAGS = ${JAVA_CPPFLAGS}|g"  "${file}" > "${file}.new"
    if test -f "${file}.new"; then
	mv "${file}.new" "${file}"
    else
	echo "*** cannot create ${file}.new~*** Please run as root if required.~" | ${SED-sed} -e 'y/~/\n/' >&2
	exit 1
    fi
done

echo "Done."
echo ''

### Local Variables: ***
### mode: sh ***
### sh-indentation: 2 ***
### End: ***