reduce firxes for bug 280857 & 280858

5 files changed, 141 insertions, 0 deletions

diff --git a/sci-chemistry/reduce/ChangeLog b/sci-chemistry/reduce/ChangeLog
new file mode 100644
index 000000000..a83360c9c
--- /dev/null
+++ b/sci-chemistry/reduce/ChangeLog
@@ -0,0 +1,66 @@
+# ChangeLog for sci-chemistry/reduce
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/ChangeLog,v 1.12 2009/05/29 00:43:56 dberkholz Exp $
+
+*reduce-3.13.080428-r1 (09 Aug 2009)
+
+  09 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/3.13.080428-LDFLAGS.patch, +reduce-3.13.080428-r1.ebuild,
+  +metadata.xml:
+  respecting LDFALGS now bug #280858
+  using right dict location during compilation bug #280857
+
+  29 May 2009; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-3.13.080428.ebuild:
+  Stable on amd64.
+
+*reduce-3.13.080428 (07 Jul 2008)
+
+  07 Jul 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  +reduce-3.13.080428.ebuild:
+  (#230693) Bump. Keyword ~amd64. Thanks to Philipp Psurek for doing the
+  initial investigation on what changes happened.
+
+  23 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-2.21.030604.ebuild, reduce-3.02.060709.ebuild:
+  (#152424) Missing dep on unzip.
+
+  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  (#148281) Change herd to sci-chemistry from sci.
+
+  30 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-3.02.060709.ebuild:
+  Directory names changed in the tarball, causing breakage. Fix it.
+
+  20 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/3.02.060709-remove-extra-qualification.patch:
+  (#143858) Add a forgotten patch.
+
+*reduce-3.02.060709 (09 Aug 2006)
+
+  09 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +reduce-3.02.060709.ebuild:
+  Bump.
+
+  09 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-2.21.030604.ebuild:
+  Update SRC_URI.
+
+  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Remove myself as maintainer, anyone feel free to work on this, although I'll
+  continue to do so as well.
+
+  09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-2.21.030604.ebuild:
+  x86/ppc stable.
+
+  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Update to my new email address.
+
+*reduce-2.21.030604 (04 Jun 2006)
+
+  04 Jun 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/2.21.030604-gcc4.patch, +metadata.xml, +reduce-2.21.030604.ebuild:
+  New package to add hydrogens to a Protein Data Bank (PDB) molecule structure
+  file.
+
diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
new file mode 100644
index 000000000..95b5bb8af
--- /dev/null
+++ b/sci-chemistry/reduce/Manifest
@@ -0,0 +1,5 @@
+AUX 3.13.080428-LDFLAGS.patch 302 RMD160 c53618b825157b1ff6bd46ac1900922a153ec622 SHA1 41cfa868a5aeca7636ff73035cf330372fdb5406 SHA256 b5299b5761bac75bb2f60392c764fefbbf397afeb32b3b08aca19889398ea291
+DIST reduce.3.13.080428.src.tgz 4387407 RMD160 b68637246dd579021cf605278690dfcb0d0074d5 SHA1 0b8142ffc4374fd7d259216fc86eb2ca94c5ea84 SHA256 6290dad33e395c5a40fe3634db86fb6035ea88ce19c3f25b80fb6378507ac066
+EBUILD reduce-3.13.080428-r1.ebuild 1197 RMD160 79debfd3309d4f90745e060dbec8d1bcc8c1ae83 SHA1 4c69b0135398659bf0094bc0af1e3b1d7bbbf31f SHA256 28961de739b2f4db658da979a640a1258cfedc3f9fc24782b1304b711fd8ec73
+MISC ChangeLog 2278 RMD160 f1f7f48ca66e3558b8d38f30c9c924d2dd87b9e0 SHA1 219c1cda0f49530a8697850715618207b35cb3e0 SHA256 f06d50a4c308291aa9f0b743d01a018e6f3d0895f2ef0aabfcfd64fe664176f8
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
new file mode 100644
index 000000000..bcee1a9fe
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
@@ -0,0 +1,11 @@
+--- reduce_src/Makefile	2009-08-09 10:11:29.000000000 +0200
++++ reduce_src/Makefile.new	2009-08-09 10:13:31.000000000 +0200
+@@ -34,7 +34,7 @@
+ all:    reduce
+ 
+ reduce: $(OBJLIST)
+-	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
++	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS)
+ 
+ clean:
+ 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml
new file mode 100644
index 000000000..9ac9ffdb3
--- /dev/null
+++ b/sci-chemistry/reduce/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
new file mode 100644
index 000000000..e1eba9983
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit base toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-LDFLAGS.patch
+	)
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FILE="reduce_het_dict.txt"
+
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${DICT_DIR}/${DICT_FILE}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce || die
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FILE} "${S}"/reduce_wwPDB_het_dict.txt || die
+	dodoc README.usingReduce.txt || die
+}
+
+pkg_info() {
+	elog "To use the PDBv3 dictionary instead of PDBv2, set the environment"
+	elog "variable REDUCE_HET_DICT to /usr/share/reduce/reduce_wwPDB_het_dict.txt"
+}
+
+pkg_postinst() {
+	pkg_info
+}