academic/mkDSSP. update for version 4.0_git6338c83

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

4 files changed, 28 insertions, 127 deletions

diff --git a/academic/mkDSSP/makefile.patch b/academic/mkDSSP/makefile.patch
deleted file mode 100644
index 17563fde9a..0000000000
--- a/academic/mkDSSP/makefile.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-Description: assorted fixes
- [Maarten L. Hekkelman <m.hekkelman@cmbi.ru.nl>]
-  * DEST_DIR patched to DESTDIR
- .
- [Laszlo Kajan <lkajan@rostlab.org>]
-  * 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 <m.hekkelman@cmbi.ru.nl>
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- 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 4a0e714a2c..a86b22daa0 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 3f2ccdf323..43a6d3a224 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 f0b462b19c..0000000000
--- 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 <lkajan@rostlab.org>
---- a/src/utils.h
-+++ b/src/utils.h
-@@ -10,7 +10,6 @@
- #endif
- 
- #include <time.h>
--#include <boost/thread.hpp>
- #include <boost/lexical_cast.hpp>
- #include <boost/format.hpp>
- #include <boost/filesystem.hpp>
---- a/src/structure.cpp
-+++ b/src/structure.cpp
-@@ -18,6 +18,7 @@
- #define foreach BOOST_FOREACH
- #include <boost/algorithm/string.hpp>
- #include <boost/math/special_functions/round.hpp>
-+#include <boost/thread.hpp>
- 
- #include "align-2d.h"
- #include "utils.h"