academic/vcftools: Updated for version 0.1.14_2_g78add55.

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

academic/vcftools/slack-desc

@@ -15,5 +15,5 @@ vcftools: VCF files: validating, merging, comparing and calculate some
 vcftools: basic population genetic statistics.
 vcftools:
 vcftools: Home: http://vcftools.sourceforge.net/
-vcftools: References: /usr/doc/vcftools-0.1.12b/References
+vcftools: References: /usr/doc/vcftools-0.1.14_2_g78add55/References
 vcftools:

academic/vcftools/use-dpkg-buildflags.patch

@@ -1,40 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Date: Sat, 12 May 2012 09:31:58 +0200
-Description: Enable propagation of hardening flags
-
-Index: vcftools_0.1.11/cpp/Makefile
-===================================================================
---- vcftools_0.1.11.orig/cpp/Makefile	2013-06-13 16:40:54.000000000 +0200
-+++ vcftools_0.1.11/cpp/Makefile	2013-06-27 19:54:45.000000000 +0200
-@@ -12,9 +12,9 @@
- 	VCFTOOLS_PCA = 0
- endif
- # Compiler flags
--CFLAGS = -O2 -m64
-+CFLAGS += -O2
- #CFLAGS = -Wall -O2 -pg -m64
--CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 
-+CPPFLAGS += -O2 -D_FILE_OFFSET_BITS=64
- #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
- # Included libraries (zlib)
- LIB = -lz 
-@@ -38,7 +38,7 @@
- endif
- 
- vcftools: $(OBJS)
--	$(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
-+	$(CPP) $(CPPFLAGS) $(OBJS) $(LDFLAGS) -o vcftools $(LIB)
- ifdef BINDIR
- 	cp $(CURDIR)/$@ $(BINDIR)/$@
- endif
-@@ -50,8 +50,8 @@
- -include $(OBJS:.o=.d)
- 
- %.o: %.cpp
--	$(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
--	$(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
-+	$(CPP) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp -o $*.o
-+	$(CPP) -MM $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $*.cpp > $*.d
- 
- # remove compilation products
- clean:

academic/vcftools/vcftools.SlackBuild

@@ -23,10 +23,13 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=vcftools
-VERSION=${VERSION:-0.1.12b}
+VERSION=${VERSION:-0.1.14_2_g78add55}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
+SRCVER=v0.1.14-2-g78add55
+GITVER=78add55
+
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
     i?86) ARCH=i486 ;;
@@ -59,9 +62,9 @@ set -e
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf ${PRGNAM}_${VERSION}
+rm -rf ${PRGNAM}-${PRGNAM}-${SRCVER}
-tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz
+tar xvf $CWD/${PRGNAM}-${PRGNAM}-${SRCVER}.tar.gz
-cd ${PRGNAM}_${VERSION}
+cd ${PRGNAM}-${PRGNAM}-${GITVER}
 chown -R root:root .
 find -L . \
  \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@@ -69,21 +72,19 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Thanks to Debian for the patch
+./autogen.sh
-patch -p1 -i $CWD/use-dpkg-buildflags.patch
-
-# Set the proper, architecture-specific path
-sed -i "s:/lib/perl5/site_perl:/lib${LIBDIRSUFFIX}/perl5:g" Makefile
-
 CFLAGS="$SLKCFLAGS" \
 CPPFLAGS="$SLKCFLAGS" \
-PREFIX=$PKG/usr \
+./configure \
-make install
+  --prefix=/usr \
-
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
-# Remove this and copy the man page to its proper place
+  --sysconfdir=/etc \
-rm -rf $PKG/usr/bin/man1
+  --localstatedir=/var \
-mkdir -p $PKG//usr/man/man1
+  --mandir=/usr/man \
-cp cpp/vcftools.1 $PKG/usr/man/man1
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+make
+make DESTDIR=$PKG install
 
 # Copy examples
 mkdir -p $PKG/usr/share/$PRGNAM
@@ -96,7 +97,7 @@ 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
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
-cp -a README.txt perl/ChangeLog website/*.pdf $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a README.md src/perl/ChangeLog $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
 

academic/vcftools/vcftools.info

@@ -1,8 +1,8 @@
 PRGNAM="vcftools"
-VERSION="0.1.12b"
+VERSION="0.1.14_2_g78add55"
-HOMEPAGE="http://vcftools.sourceforge.net/"
+HOMEPAGE="https://vcftools.github.io/"
-DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12b.tar.gz"
+DOWNLOAD="https://github.com/vcftools/vcftools/tarball/master/vcftools-vcftools-v0.1.14-2-g78add55.tar.gz"
-MD5SUM="662758d1139c138cf5a0239ed99f12c2"
+MD5SUM="e5fbb773ef13d567606067351501ac13"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="tabix"