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author Rob van Nues <sborg63@disroot.org>2019-07-13 08:25:08 +0700
committer Willy Sudiarto Raharjo <willysr@slackbuilds.org>2019-07-13 08:25:23 +0700
commitf383bf9d2ceffa3b5bbea777fd14dae9ce0fb5af (patch)
treeb821b9dda2c7b1609814db45e8ddd8f44194db2d /academic/ViennaRNA/ViennaRNA.SlackBuild
parent543a2f92ac942e08e784a6be7292c35e58eee05a (diff)
downloadslackbuilds-f383bf9d2ceffa3b5bbea777fd14dae9ce0fb5af.tar.gz
slackbuilds-f383bf9d2ceffa3b5bbea777fd14dae9ce0fb5af.tar.xz
academic/ViennaRNA: Updated for version 2.4.13.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/ViennaRNA/ViennaRNA.SlackBuild')
-rw-r--r--academic/ViennaRNA/ViennaRNA.SlackBuild46
1 files changed, 26 insertions, 20 deletions
diff --git a/academic/ViennaRNA/ViennaRNA.SlackBuild b/academic/ViennaRNA/ViennaRNA.SlackBuild
index 9de92bfa6e..5b8a1882a2 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