ap/EMBOSS: Upgraded to EMBOSS-6.3.1.

ap/EMBOSS/EMBOSS-6.3.1.tar.gz.sha1

@@ -0,0 +1 @@
+efb2e9c1c9b038432ce6bd81ee4692d5f1dc2f72  EMBOSS-6.3.1.tar.gz

ap/EMBOSS/EMBOSS.SlackBuild

@@ -29,13 +29,13 @@
 
 # Source package infos
 NAMESRC=${NAMESRC:-EMBOSS}
-VERSION=${VERSION:-6.2.0}
+VERSION=${VERSION:-6.3.1}
 ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
 WGET=${WGET:-ftp://emboss.open-bio.org/pub/EMBOSS/$ARCHIVE}
 
 # Build infos
 NAMEPKG=${NAMEPKG:-EMBOSS}
-BUILD=${BUILD:-2GGD}
+BUILD=${BUILD:-1GGD}
 ARCH=${ARCH:-$(uname -m | sed 's/^i?86$/i486/;s/^arm.*/arm/')}
 EXT=${EXT:-txz}
 JOBS=${JOBS:-1}
@@ -94,11 +94,6 @@ if [ ! -r rebase.tar.gz ]; then
 fi
 
 # Compile
-# EMBOSS insists on using its own copies of some available libraries
-# such as zlib, expat and pcre. I do not want to start patching the
-# build system heavily (as Debian or Fedora seem to do), so at least
-# I need to prevent replacing the system headers, hence the
-# --includedir=/usr/include/EMBOSS to isolate EMBOSS headers.
 cd $TMP
 echo "Building $ARCHIVE..."
 tar xf $CWD/$ARCHIVE
@@ -112,6 +107,7 @@ CXXFLAGS=$CPUOPT \
   $ENABLE64 \
   --disable-dependency-tracking \
   --disable-static \
+  --enable-systemlibs \
   --with-java=/usr/lib$LIBDIRSUFFIX/jdk$JDKVERSION/include \
   --with-javaos=/usr/lib$LIBDIRSUFFIX/jdk$JDKVERSION/include/linux
 make -j $JOBS
@@ -119,10 +115,8 @@ make install-strip DESTDIR=$PKG
 
 # Install the documentation
 mkdir -p $PKG/usr/doc/$NAME
-install -m 644 \
-  AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS ONEWS \
-  PROBLEMS README THANKS \
-  $PKG/usr/doc/$NAME
+install -m 644 AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS \
+  ONEWS PROBLEMS README THANKS $PKG/usr/doc/$NAME
 
 # Install REBASE data
 tar xf $CWD/rebase.tar.gz -C $PKG/usr/share/EMBOSS/data/REBASE