diff options
| -rw-r--r-- | academic/vcftools/slack-desc | 2 | ||||
| -rw-r--r-- | academic/vcftools/use-dpkg-buildflags.patch | 40 | ||||
| -rw-r--r-- | academic/vcftools/vcftools.SlackBuild | 37 | ||||
| -rw-r--r-- | academic/vcftools/vcftools.info | 8 |
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" |