academic/ViennaRNA: Updated for version 2.4.13.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 26 insertions, 20 deletions

diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild
index 9de92bfa6e872..5b8a1882a26da 100644
--- a/academic/ViennaRNA/ViennaRNA.SlackBuild
+++ b/academic/ViennaRNA/ViennaRNA.SlackBuild
@@ -23,13 +23,13 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=ViennaRNA
-VERSION=${VERSION:-2.4.12}
+VERSION=${VERSION:-2.4.13}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i486 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
        *) ARCH=$( uname -m ) ;;
   esac
@@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
   LIBDIRSUFFIX=""
 elif [ "$ARCH" = "i686" ]; then
   SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@@ -63,16 +63,11 @@ rm -rf $PRGNAM-$VERSION
 tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM-$VERSION
 chown -R root:root .
-find . \
- \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
- 
-patch -p 1 < $CWD/swig4.patch
-
-#needed to make patches compile
-autoreconf
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
 # You can configure some ViennaRNA features that are (not) compiled by default.
 # See the README.md for details. You can enable/disable a these features by
@@ -107,7 +102,7 @@ forester=""      ; [ "${FORESTER:-yes}" != "yes" ]     && forester="--without-fo
 kinfold=""       ; [ "${KINFOLD:-yes}" != "yes" ]     && kinwalk="--without-kinfold"
 rnalocmin=""     ; [ "${RNALOCMIN:-yes}" != "yes" ]     && rnalocmin="--without-rnalocmin"
 perl=""          ; [ "${PERL:-yes}" != "yes" ]     && perl="--without-perl"
-python=""        ; [ "${PYTHON:-yes}" != "yes" ]     && python="--without-python"
+
 python3=""       ; [ "${PYTHON3:-yes}" != "yes" ]     && python3="--without-python3"
 swig=""          ; [ "${SWIG:-yes}" != "yes" ]     && swig="--without-swig"
 simd=""          ; [ "${SIMD:-yes}" != "yes" ]     && simd="--disable-simd"
@@ -116,6 +111,8 @@ openmp=""        ; [ "${OPENMP:-yes}" != "yes" ]      && openmp="--disable-openm
 pthreads=""      ; [ "${PTHREADS:-yes}" != "yes" ]     && pthreads="--disable-pthreads"
 svm=""           ; [ "${SVM:-yes}" != "yes" ]      && svm="--without-svm"
 gsl=""           ; [ "${GSL:-yes}" != "yes" ]      && gsl="--without-gsl"
+# Default to python3 (above) only;
+python=""        ; [ "${PYTHON:-no}" != "yes" ]     && python="--without-python"
 
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
@@ -149,12 +146,14 @@ cd misc
 make install DESTDIR=$PKG
 cd ..
 
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
 # cleanup after dirty install ...
-#  install -dm755 $PKG/usr/bin/vendor_perl
 for perlscript in $PKG/usr/share/ViennaRNA/bin/*.pl ; do
-#    mv "$perlscript" "$PKG/usr/bin/vendor_perl/"
     mv "$perlscript" "$PKG/usr/bin/"
 done
+rm -r $PKG/usr/share/ViennaRNA/bin
 
 # no need for that file it is outdated anyway
 rm $PKG/usr/share/info/dir
@@ -162,9 +161,6 @@ rm $PKG/usr/share/info/dir
 #gzip info file
 gzip -9 $PKG/usr/share/info/*.info
 
-find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
-  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
-
 find $PKG/usr/man -type f -exec gzip -9 {} \;
 for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
 
@@ -174,6 +170,16 @@ find $PKG -name perllocal.pod \
   | xargs rm -f
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+
+#keep help and RNAlib-${VERSION} in src
+if [[ -d $PKG/usr/doc/$PRGNAM-$VERSION/html ]]; then
+ rm -r $PKG/usr/doc/$PRGNAM-$VERSION/html
+fi
+
+if [[ -e $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf ]]; then
+ rm $PKG/usr/doc/$PRGNAM-$VERSION/RNAlib-$VERSION.pdf
+fi
+
 cp -a \
   NEWS README.md AUTHORS COPYING THANKS INSTALL CHANGELOG.md license.txt \
   $PKG/usr/doc/$PRGNAM-$VERSION