Clean old versions, fix for bug 280857 & bug 280858

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

6 files changed, 83 insertions, 123 deletions

diff --git a/sci-chemistry/reduce/ChangeLog b/sci-chemistry/reduce/ChangeLog
index f357c8aaee35..ccdf4e1c5d70 100644
--- a/sci-chemistry/reduce/ChangeLog
+++ b/sci-chemistry/reduce/ChangeLog
@@ -1,6 +1,13 @@
 # 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 $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/ChangeLog,v 1.13 2010/02/05 23:41:04 jlec Exp $
+
+*reduce-3.13.080428-r1 (05 Feb 2010)
+
+  05 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/3.13.080428-LDFLAGS.patch, -reduce-2.21.030604.ebuild,
+  -reduce-3.02.060709.ebuild, +reduce-3.13.080428-r1.ebuild:
+  Clean old versions, fix for 280857 & 280858
 
   29 May 2009; Donnie Berkholz <dberkholz@gentoo.org>;
   reduce-3.13.080428.ebuild:
diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
index 694208e06603..433ea67db520 100644
--- a/sci-chemistry/reduce/Manifest
+++ b/sci-chemistry/reduce/Manifest
@@ -3,19 +3,16 @@ Hash: SHA1
 
 AUX 2.21.030604-gcc4.patch 3946 RMD160 f9c8d7f884bc942e31bd0273fe4f43d8f0e2ecc6 SHA1 c596c6ac2741567bc179e50871cc3d607327cec1 SHA256 9c6372e7d44ff83b42ab0ad7f08b7173c8cbfabe204b991ec828c5428d048ff8
 AUX 3.02.060709-remove-extra-qualification.patch 511 RMD160 6c3d43d39a40c608e9aad6ad9fe6da06b59f98e6 SHA1 48805fa78b64f4ab1f46c1acf51eb85032af8db8 SHA256 c814e0e6f23671aba5e2d1b6be74f91390737bd06ca7fbc122ef31eec0ae4c28
-DIST reduce.2.21.030604.src.tgz 132262 RMD160 db5ff4ea12e50c7ea9d8215011f80966ce5397b6 SHA1 c69944bb28beb50013e8c8b6ea67d2581e924777 SHA256 0889c1bed10680090a1fd62cce1a46a13768b4ea77cbf036245b15e2e542337d
-DIST reduce.3.02.060709.source.tgz 1266648 RMD160 2ea7cca496901fa3e7e4975bcd6fce4fba17ff44 SHA1 491bd499ca1d935f36bc2c134c2e2f92aa8205bb SHA256 bd134c3e5859a6ec361b1c07405d17c3ffc14cfcb26ebbe439d1cfe07208a275
+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
-DIST reduce_het_dict.txt.zip 983850 RMD160 5d1aa16adc4c9e3355b58937dbe8033afa4e8a17 SHA1 13a73d98315deef4abc76afa3cb5b7dc775c3882 SHA256 382802ebb89332dd0a0f208ef5ca6b9cd0ddca5b7a5d6bf8226d5aa1f506a384
-EBUILD reduce-2.21.030604.ebuild 1699 RMD160 5a6ce5ed7ac3b9f1dc80f159e8fded46e76407d4 SHA1 170f27cb7cee5b119e13c138565257a245004283 SHA256 aaa3a65b3e264d0c342202c8cb113e4c33be8e3147c00f8868357047357e8d39
-EBUILD reduce-3.02.060709.ebuild 1395 RMD160 d206b17dc9610ab57a8d4b86ca057ae95c4aeab9 SHA1 2f6008c2c2a2b858495906478e1a42e17d2258e8 SHA256 91efa4d264990ab60fc8ba0da2fa4d17d4af51c848b2e57e318e4ed181c679f1
+EBUILD reduce-3.13.080428-r1.ebuild 1341 RMD160 2ee4dcc28e1fd212f597a6d7d97552e0094819db SHA1 774f1478c4264582523c73a3571fdd28addace90 SHA256 b6de2edc594c5318474bd4f11cdd354872425f19009371156c28e579e4c89629
 EBUILD reduce-3.13.080428.ebuild 1536 RMD160 ee165a8c59c415ed6e0df56522520c554e18a7f0 SHA1 f7249fa47c1090dbc95da24308930c5d1e36956b SHA256 c795681d433dc3bbb9163c66c2198d9b7844e0ce3a18dde34dd25c9a6b546bfb
-MISC ChangeLog 2002 RMD160 6526221d078ffe1a46fce3bf942c3a911f462a1e SHA1 7271540beb5425f183596fc357366a762c28d4bc SHA256 7c0d4807657d5552104ed6ac833c327eeca298e449235cf745b5cd126c795ad2
+MISC ChangeLog 2261 RMD160 b2519914fe2950dbece3204f686be826bb6762ca SHA1 ec4fe42f84d5f516a5ee3daa03817c4c8c9eb7e0 SHA256 f3c4c3d8a10195954eecf563a291815a5a122b1806358413a820cab0fb91cc14
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
+Version: GnuPG v2.0.14 (GNU/Linux)
 
-iEYEARECAAYFAkofL9IACgkQXVaO67S1rttijgCg85G9/VJam87I6KpH5m6t8PIX
-MkAAoIVFnbtVA1LgNUy+1nqjxtWAfk2S
-=bDdw
+iEYEARECAAYFAktsrJUACgkQgAnW8HDreRamFACeKSyxR58S/El22EjFRMXegqGl
+zrUAn0b/KhNl4n3lmRU57QNsk9AVrnXB
+=q4xP
 -----END PGP SIGNATURE-----
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 000000000000..bcee1a9fe8f3
--- /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/reduce-2.21.030604.ebuild b/sci-chemistry/reduce/reduce-2.21.030604.ebuild
deleted file mode 100644
index d101a977f163..000000000000
--- a/sci-chemistry/reduce/reduce-2.21.030604.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-2.21.030604.ebuild,v 1.4 2006/10/23 03:55:16 dberkholz Exp $
-
-# If you want to fix the warnings about friend declaration 'foo' declared as
-# a non-template function, see http://gcc.gnu.org/faq.html#friend.
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}.${PV}"
-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/reduce/${MY_P}.src.tgz
-	http://kinemage.biochem.duke.edu/downloads/software/reduce/reduce_het_dict.txt.zip"
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="ppc x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-S="${WORKDIR}/${MY_P}.source"
-
-src_unpack() {
-	DICT_DIR="/usr/$(get_libdir)/reduce"
-	DICT_FILE="reduce_het_dict.txt"
-	DICT_LOC="${DICT_DIR}/${DICT_FILE}"
-
-	unpack ${A}
-	epatch ${FILESDIR}/${PV}-gcc4.patch
-
-	# Get Makefiles that are at least somewhere close to right
-	einfo "Updating Makefiles"
-	for dir in libpdb reduce_src toolclasses; do
-		pushd "${S}"/${dir} > /dev/null
-		mv Makefile Makefile.old
-		mv Makefile.g++ Makefile
-		popd > /dev/null
-	done
-
-	# Do after replacing Makefiles
-	einfo "Fixing CFLAGS and locations"
-	sed -i \
-		-e "s:^\(DICT_HOME\).*:\1 = ${DICT_LOC}:g" \
-		-e "s:-DBRACKETOPERPARMS::g" \
-		"${S}"/*/Makefile
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin ${S}/reduce_src/reduce
-	dodoc ${S}/README*
-	insinto ${DICT_DIR}
-	doins ${WORKDIR}/${DICT_FILE}
-}
diff --git a/sci-chemistry/reduce/reduce-3.02.060709.ebuild b/sci-chemistry/reduce/reduce-3.02.060709.ebuild
deleted file mode 100644
index 6499a9ba82f2..000000000000
--- a/sci-chemistry/reduce/reduce-3.02.060709.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-3.02.060709.ebuild,v 1.3 2006/10/23 03:55:16 dberkholz Exp $
-
-# If you want to fix the warnings about friend declaration 'foo' declared as
-# a non-template function, see http://gcc.gnu.org/faq.html#friend.
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}.${PV}.source"
-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/reduce/${MY_P}.tgz
-	http://kinemage.biochem.duke.edu/downloads/software/reduce/reduce_het_dict.txt.zip"
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-S="${WORKDIR}/${PN}src"
-
-src_unpack() {
-	DICT_DIR="/usr/share/reduce"
-	DICT_FILE="reduce_het_dict.txt"
-	DICT_LOC="${DICT_DIR}/${DICT_FILE}"
-
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PV}-remove-extra-qualification.patch
-
-	einfo "Fixing location of dictionary"
-	sed -i \
-		-e "s:^\(DICT_HOME.*=\).*:\1 ${DICT_LOC}:g" \
-		"${S}"/*/Makefile
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin ${S}/reduce_src/reduce
-	insinto ${DICT_DIR}
-	doins ${WORKDIR}/${DICT_FILE}
-}
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 000000000000..a4c7ea549cb7
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild,v 1.1 2010/02/05 23:41:04 jlec Exp $
+
+EAPI="3"
+
+inherit eutils 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}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-LDFLAGS.patch
+}
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FILE="reduce_het_dict.txt"
+
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${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
+}