reinit the tree, so we can have metadata

6 files changed, 137 insertions, 0 deletions

diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest
new file mode 100644
index 000000000000..0834ad49df66
--- /dev/null
+++ b/sci-chemistry/cluster/Manifest
@@ -0,0 +1,8 @@
+AUX 1.3.081231-includes.patch 245 SHA256 a4ab35ecef5f3bc2146823f6bd611f2a7dc0dc1fa299cb60f2c8a94ff64e78ae SHA512 a1261ed2b3f867fe464e1501fa9bc0b1f2909eaf736475e717da95ddbc34ae2938346c0044f7b6d84264a0d85ea5f7b1214caf1c2b12c544876912ff10e2302a WHIRLPOOL b39276b9aa98fd9c81b0bfbfddcc7573c3c43d1b3638556b8a911be66006cb81b15d9f8f05cfdc0b073c32950e70c4d115f8122cd7e4d3b8c6ef55e5beb51271
+AUX 1.3.081231-ldflags.patch 842 SHA256 32d3d0821d1366af28553c1f3a28f5e6f9b1ea593b7c21efb30d478080219f2f SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4 WHIRLPOOL 7af94b4a1d1375785e200ebe4bdcd91e4ba2ee6aca0d19188cb924465c29a02ee4775326aea4bdef11fbe9fe068312d4c248ef2b56c2357217a64d2c658166c2
+DIST cluster.1.3.081231.src.tgz 8860 SHA256 4e0986d5ff124936b5fff4b6f8989dd04be11180d6552fddc34b2c10dfcc870f SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac WHIRLPOOL 2f02de20b323792360b28d5a42d233d06be529414e29796a39a439651fee9e8ba73bdd05033907ac7434890bfa2a31aaf57ab98bbe59964d06a2d63646833f5f
+EBUILD cluster-1.3.081231-r1.ebuild 664 SHA256 1e4f87963d752f207938865011496e5ec461b69614e561d2cf57582f5042c5e4 SHA512 2179d4beb99e86945b2afa8b0951da4f2c59ad13a0070429d7c0a24e0d363ee0a7f12a3710655305be332cec4744e3b22167e1c99986fcb1e22dec2fc46e6d59 WHIRLPOOL 820b6e31cb52ef88027a7e2c62524d4ef03d5de900921c8e6fd8873af7a94e0fe3927f2b00449a7375f800cea640ebec82141cdaab24b3605fbdc2d9a0a3f304
+EBUILD cluster-1.3.081231.ebuild 646 SHA256 c11080dcd466c8346e3f0a709fec5a0edd289eedea63ece008683ea8ee14a46c SHA512 2bafc4cec0e46ad3749a5b005f629340bc2b0ec8e3fd062da5f20edcccb67597c6a3b1cb5c7045a2d3796de3b488f78ca7b53678c911d63f9dfaf0ff290f9a73 WHIRLPOOL 9818aacf36464c6a282f7468c0f3c17261a85760dbc0f82032cddd7daf63b37c960fe5e2754695bc2ce978916e8d0fb9ee3d6e277604c54cfa53bb1322b2e0db
+MISC ChangeLog 2721 SHA256 b8594c90a8f6d0985eb00aa67d89994a5c1d39c52f580285b7e8a3866120b630 SHA512 3588e18b2936a2133f1905eeda0f7a51dbbd73748f6693a18ade4dc22d7e22cccfeaaa664029c49d2da2f528acf79ff1280d806737f33b7a09afcfe649504cea WHIRLPOOL c723e15094658deee98aea4011629935ff445890fdad7fe97183d09f4bec60298dd91a91f94d935aeec48cee0342dc283be634a5105eda1db386dfadce41a486
+MISC ChangeLog-2015 1628 SHA256 1f8d4eb64bc6a4286abef1c5ff341bab34e634aa44ccede53ddedbfef659436c SHA512 836be8b404b2322513fad122319a5a73dcca232db1dd328e2d6c7bf3259fdea0ead351274d68c611837fb209ba1e3f4bb70cd3e826a997cfcae4355015a70bf9 WHIRLPOOL e51962bb7b1782f0b813fbd90d6aa4b74fa915cc6a48e6a061a69a91fbfb0abb9a99b248d09ebce1001dd1e811e4c5272ba1f04b3dd37ebdedc75ba106e803e7
+MISC metadata.xml 661 SHA256 5e895ff55256c3017a244b7bfd59dc8a8de3aa6d5601341155aba0468ab3bd2c SHA512 449c8965bd2f3039effcf1d6fc15fea1708cf5987aee36a4b8c470f85b59f7b04884a796a353f17fd890aa9d2e4ee7b1c25ed969febabaa54e577f8be31ed889 WHIRLPOOL edd65cfb23cb24fee72d2c940ad88e5c9186f2b6a1d390d4c29f1d93314a2ef7f068032b72b1d8bbea7d7ca565941eafe8a49715e5ac05d5c0f97dcbf88939f8
diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
new file mode 100644
index 000000000000..955f546926e2
--- /dev/null
+++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Build lists of collections of interacting items"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
+
+SLOT="0"
+LICENSE="richardson"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+S="${WORKDIR}"/${PN}1.3src
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-ldflags.patch \
+		"${FILESDIR}"/${PV}-includes.patch
+	tc-export CXX
+}
+
+src_install() {
+	newbin ${PN} molprobity-${PN}
+	dodoc README.cluster
+}
diff --git a/sci-chemistry/cluster/cluster-1.3.081231.ebuild b/sci-chemistry/cluster/cluster-1.3.081231.ebuild
new file mode 100644
index 000000000000..e9d3b8999e1e
--- /dev/null
+++ b/sci-chemistry/cluster/cluster-1.3.081231.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Build lists of collections of interacting items"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
+
+SLOT="0"
+LICENSE="richardson"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+S="${WORKDIR}"/${PN}1.3src
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-ldflags.patch \
+		"${FILESDIR}"/${PV}-includes.patch
+	tc-export CXX
+}
+
+src_install() {
+	dobin ${PN}
+	dodoc README.cluster
+}
diff --git a/sci-chemistry/cluster/files/1.3.081231-includes.patch b/sci-chemistry/cluster/files/1.3.081231-includes.patch
new file mode 100644
index 000000000000..a5586a540a4f
--- /dev/null
+++ b/sci-chemistry/cluster/files/1.3.081231-includes.patch
@@ -0,0 +1,12 @@
+diff --git a/cluster.cpp b/cluster.cpp
+index 0a8c3c1..1384949 100644
+--- a/cluster.cpp
++++ b/cluster.cpp
+@@ -24,6 +24,7 @@
+ #include <iostream>
+ #include <vector>
+ #include <string>
++#include <cstring>
+ 
+ #include <iostream>
+ #include <fstream>
diff --git a/sci-chemistry/cluster/files/1.3.081231-ldflags.patch b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch
new file mode 100644
index 000000000000..1b99f6d662f2
--- /dev/null
+++ b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch
@@ -0,0 +1,41 @@
+ Makefile |   12 ++++++------
+ 1 files changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 7892054..929564b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -3,27 +3,27 @@ PROG_FLGS   = -D BOOLPREDEFINED
+ 
+ SRCS = cluster.cpp DisjointSets.cpp utility.cpp
+ 
+-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS)
++CXXFLAGS += $(OPT) $(DEBUG) $(PROG_FLGS)
+ 
+ LFLAGS = 
+ 
+ OBJLIST = cluster.o DisjointSets.o utility.o
+ 
+-CXX		= g++
++CXX		?= g++
+ 
+ .cpp.o:
+-	$(CXX) -c $*.cpp $(CFLAGS)
++	$(CXX) $(CXXFLAGS) -c $*.cpp
+ 
+-OPT             = -O3
++OPT             = 
+ DEBUG           = $(CXXDEBUGFLAGS)
+ 
+ all:    cluster
+ 
+ cluster:    $(OBJLIST)
+-	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
++	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST)
+ 
+ depend:
+-	makedepend -- $(CFLAGS) -- $(SRCS)
++	makedepend -- $(CXXFLAGS) -- $(SRCS)
+ 
+ clean:
+ 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/cluster/metadata.xml b/sci-chemistry/cluster/metadata.xml
new file mode 100644
index 000000000000..62f5e4eb25ab
--- /dev/null
+++ b/sci-chemistry/cluster/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <longdescription>
+Cluster is a simple UNIX C++ program to build lists of collections
+of interacting items from records containing interacting pairs
+and larger fragments.
+
+It reads in lines consisting of two or more names and output
+connected clusters of names. Each line of output is
+prefixed with a cluster number, the size of the cluster
+and an optional name string.
+</longdescription>
+</pkgmetadata>