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authorPetar Petrov <petar.petrov@student.oulu.fi>2015-11-11 23:12:27 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2015-11-11 23:12:27 +0700
commit72a5c0c201318280dea8d10ef53a3adb7edcf4ca (patch)
tree2b35c0bb039e116f0bef792b2a6e7c6835aa0544 /academic
parentc61d2947f7e9850d8d9166d610bfbedb3d16b36e (diff)
downloadslackbuilds-72a5c0c201318280dea8d10ef53a3adb7edcf4ca.tar.gz
academic/vcftools: Updated for version 0.1.14_2_g78add55.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/vcftools/slack-desc2
-rw-r--r--academic/vcftools/use-dpkg-buildflags.patch40
-rw-r--r--academic/vcftools/vcftools.SlackBuild37
-rw-r--r--academic/vcftools/vcftools.info8
4 files changed, 24 insertions, 63 deletions
diff --git a/academic/vcftools/slack-desc b/academic/vcftools/slack-desc
index 7cbadbcbbf..50dac51d10 100644
--- a/academic/vcftools/slack-desc
+++ b/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:
diff --git a/academic/vcftools/use-dpkg-buildflags.patch b/academic/vcftools/use-dpkg-buildflags.patch
deleted file mode 100644
index 3bd8521a3a..0000000000
--- a/academic/vcftools/use-dpkg-buildflags.patch
+++ /dev/null
@@ -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 > $*.d
-
- # remove compilation products
- clean:
diff --git a/academic/vcftools/vcftools.SlackBuild b/academic/vcftools/vcftools.SlackBuild
index 624601bdb3..7cfe136df6 100644
--- a/academic/vcftools/vcftools.SlackBuild
+++ b/academic/vcftools/vcftools.SlackBuild
@@ -23,10 +23,13 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=vcftools
-VERSION=${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}
-tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz
-cd ${PRGNAM}_${VERSION}
+rm -rf ${PRGNAM}-${PRGNAM}-${SRCVER}
+tar xvf $CWD/${PRGNAM}-${PRGNAM}-${SRCVER}.tar.gz
+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
-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
-
+./autogen.sh
CFLAGS="$SLKCFLAGS" \
CPPFLAGS="$SLKCFLAGS" \
-PREFIX=$PKG/usr \
-make install
-
-# Remove this and copy the man page to its proper place
-rm -rf $PKG/usr/bin/man1
-mkdir -p $PKG//usr/man/man1
-cp cpp/vcftools.1 $PKG/usr/man/man1
+./configure \
+ --prefix=/usr \
+ --libdir=/usr/lib${LIBDIRSUFFIX} \
+ --sysconfdir=/etc \
+ --localstatedir=/var \
+ --mandir=/usr/man \
+ --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
diff --git a/academic/vcftools/vcftools.info b/academic/vcftools/vcftools.info
index e30951603f..9e3ee465af 100644
--- a/academic/vcftools/vcftools.info
+++ b/academic/vcftools/vcftools.info
@@ -1,8 +1,8 @@
PRGNAM="vcftools"
-VERSION="0.1.12b"
-HOMEPAGE="http://vcftools.sourceforge.net/"
-DOWNLOAD="http://sourceforge.net/projects/vcftools/files/vcftools_0.1.12b.tar.gz"
-MD5SUM="662758d1139c138cf5a0239ed99f12c2"
+VERSION="0.1.14_2_g78add55"
+HOMEPAGE="https://vcftools.github.io/"
+DOWNLOAD="https://github.com/vcftools/vcftools/tarball/master/vcftools-vcftools-v0.1.14-2-g78add55.tar.gz"
+MD5SUM="e5fbb773ef13d567606067351501ac13"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="tabix"