From 159c498151abfb97d93b2e4d563fae6e3a1efd05 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 18 May 2021 16:37:33 +0300 Subject: academic/mkDSSP. update for version 4.0_git6338c83 Signed-off-by: Willy Sudiarto Raharjo --- academic/mkDSSP/makefile.patch | 76 ------------------------------------ academic/mkDSSP/mkDSSP.SlackBuild | 46 +++++++++++----------- academic/mkDSSP/mkDSSP.info | 10 ++--- academic/mkDSSP/thread_include.patch | 23 ----------- 4 files changed, 28 insertions(+), 127 deletions(-) delete mode 100644 academic/mkDSSP/makefile.patch delete mode 100644 academic/mkDSSP/thread_include.patch (limited to 'academic/mkDSSP') diff --git a/academic/mkDSSP/makefile.patch b/academic/mkDSSP/makefile.patch deleted file mode 100644 index 17563fde9ab1..000000000000 --- a/academic/mkDSSP/makefile.patch +++ /dev/null @@ -1,76 +0,0 @@ -Description: assorted fixes - [Maarten L. Hekkelman ] - * DEST_DIR patched to DESTDIR - . - [Laszlo Kajan ] - * stripping is patched out so that it can be done by dh into a debug package - * line echo suppression is removed - * spelling errors in man page fixed - . - Upstream is aware of this patch. -Author: Maarten L. Hekkelman -Author: Laszlo Kajan ---- a/makefile -+++ b/makefile -@@ -11,18 +11,16 @@ - - all: mkdssp - --include make.config -- - VERSION = 2.2.1 - - DEST_DIR ?= /usr/local - LIB_DIR = $(BOOST_LIB_DIR) - INC_DIR = $(BOOST_INC_DIR) --BIN_DIR = $(DEST_DIR)/bin --MAN_DIR = $(DEST_DIR)/man/man1 -+BIN_DIR = $(DESTDIR)$(DEST_DIR)/bin -+MAN_DIR = $(DESTDIR)$(DEST_DIR)/share/man/man1 - --BOOST_LIBS = thread filesystem program_options iostreams system --LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 -+BOOST_LIBS = thread program_options iostreams system -+LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) - - DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' - CXX = g++ -@@ -49,22 +47,19 @@ - OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ_DIR)/structure.o $(OBJ_DIR)/utils.o $(OBJ_DIR)/mas.o $(OBJ_DIR)/iocif.o - - mkdssp: $(OBJECTS) -- @ echo linking $@ -- @ $(CXX) -static -o $@ $^ $(LDOPTS) -+ $(CXX) -o $@ $^ $(LDOPTS) - --include $(OBJECTS:%.o=%.d) -+-include $(OBJECTS:%.o=%.d) - - $(OBJECTS:.o=.d): - - $(OBJ_DIR): -- @ mkdir -p $(OBJ_DIR) -+ mkdir -p $(OBJ_DIR) - - $(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) -- @ echo compiling $@ -- @ $(CXX) -MD -c -o $@ $< $(CFLAGS) -+ $(CXX) -MD -c -o $@ $< $(CPPFLAGS) $(CFLAGS) - - clean: -- install -d $(BIN_DIR) $(MAN_DIR) - rm -rf $(OBJ_DIR)/* mkdssp - - install: mkdssp -@@ -85,11 +80,3 @@ - @ cp doc/mkdssp.1 $(DIST_NAME)/doc/mkdssp.1 - tar czf $(DIST_NAME).tgz $(DIST_NAME) - cp $(DIST_NAME).tgz dssp_$(VERSION).orig.tar.gz -- --make.config: -- @echo "creating empty make.config file" -- @echo "# Set local options for make here" > make.config -- @echo "#BOOST_LIB_SUFFIX = -mt" >> make.config -- @echo "#BOOST_LIB_DIR = $(HOME)/projects/boost/lib" >> make.config -- @echo "#BOOST_INC_DIR = $(HOME)/projects/boost/include" >> make.config -- diff --git a/academic/mkDSSP/mkDSSP.SlackBuild b/academic/mkDSSP/mkDSSP.SlackBuild index 4a0e714a2c7b..a86b22daa0d9 100644 --- a/academic/mkDSSP/mkDSSP.SlackBuild +++ b/academic/mkDSSP/mkDSSP.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for mkDSSP -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -23,14 +23,16 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=mkDSSP -SRCNAM=dssp -VERSION=${VERSION:-2.2.1} +VERSION=${VERSION:-4.0_git6338c83} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +SRCNAM=dssp +COMMIT="6338c836b631e87fc03bd147ec67d27ea72f6f70" + if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -41,8 +43,8 @@ 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" @@ -60,9 +62,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM-$VERSION -tar xvf $CWD/$SRCNAM-$VERSION.tgz -cd $SRCNAM-$VERSION +rm -rf $SRCNAM-$COMMIT +tar xvf $CWD/$SRCNAM-$COMMIT.tar.gz +cd $SRCNAM-$COMMIT chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -70,19 +72,20 @@ 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 patches! -patch -p1 -i $CWD/makefile.patch -patch -p1 -i $CWD/thread_include.patch - CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ -BIN_DIR=/usr/bin \ -MAN_DIR=/usr/man/man1 \ -make +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --disable-revision \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux -make install DEST_DIR=$PKG \ -BIN_DIR=$PKG/usr/bin \ -MAN_DIR=$PKG/usr/man/man1 +make +make install DESTDIR=$PKG mandir=$PKG/usr/man # Some programs (like aline) expect the binary to be called just "dssp" cd $PKG/usr/bin @@ -92,12 +95,9 @@ 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 -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 \ - changelog LICENSE_1_0.txt README.txt \ + LICENSE README.md \ $PKG/usr/doc/$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/mkDSSP/mkDSSP.info b/academic/mkDSSP/mkDSSP.info index 3f2ccdf32382..43a6d3a2245d 100644 --- a/academic/mkDSSP/mkDSSP.info +++ b/academic/mkDSSP/mkDSSP.info @@ -1,10 +1,10 @@ PRGNAM="mkDSSP" -VERSION="2.2.1" -HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" -DOWNLOAD="ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1.tgz" -MD5SUM="0faa63ea1f0c69def077530de0cf84c1" +VERSION="4.0_git6338c83" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/DSSP_3.html" +DOWNLOAD="https://github.com/PDB-REDO/dssp/archive/6338c83/dssp-6338c836b631e87fc03bd147ec67d27ea72f6f70.tar.gz" +MD5SUM="c4616197bb510c36f1c4dcce018e870d" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="libcifpp" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/mkDSSP/thread_include.patch b/academic/mkDSSP/thread_include.patch deleted file mode 100644 index f0b462b19c01..000000000000 --- a/academic/mkDSSP/thread_include.patch +++ /dev/null @@ -1,23 +0,0 @@ -Description: moving boost thread include out of header that does not use it - Patch is not yet forwarded upstream. -Author: Laszlo Kajan ---- a/src/utils.h -+++ b/src/utils.h -@@ -10,7 +10,6 @@ - #endif - - #include --#include - #include - #include - #include ---- a/src/structure.cpp -+++ b/src/structure.cpp -@@ -18,6 +18,7 @@ - #define foreach BOOST_FOREACH - #include - #include -+#include - - #include "align-2d.h" - #include "utils.h" -- cgit v1.2.3