From ccd7db51be077706c9d9e8ab3094cc0d87370c45 Mon Sep 17 00:00:00 2001
From: Justin Lecher <jlec@gentoo.org>
Date: Tue, 15 Jun 2010 14:45:45 +0000
Subject: [PATCH] qa and adopted to bug 314053 Package-Manager:
 portage-2.2_rc67/cvs/Linux x86_64

---
 sci-chemistry/pdb-extract/ChangeLog           |  8 ++-
 .../pdb-extract-3.004-cflags-install.patch    |  4 +-
 .../pdb-extract/pdb-extract-3.004-r2.ebuild   | 70 +++++++++++++++++++
 sci-chemistry/scala/Manifest                  | 10 +--
 4 files changed, 84 insertions(+), 8 deletions(-)
 create mode 100644 sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild

diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog
index b8496aceea92..b9c98dda5f0e 100644
--- a/sci-chemistry/pdb-extract/ChangeLog
+++ b/sci-chemistry/pdb-extract/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb-extract
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.15 2010/04/25 09:53:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.16 2010/06/15 14:45:45 jlec Exp $
+
+*pdb-extract-3.004-r2 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org> +pdb-extract-3.004-r2.ebuild,
+  files/pdb-extract-3.004-cflags-install.patch:
+  qa and adopted to bug 314053
 
 *pdb-extract-3.004-r1 (25 Apr 2010)
 
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
index 1b60778ce97c..cdf48e4784c6 100644
--- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
@@ -59,7 +59,7 @@ diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004
  ##
  ##########################################################################
  
-+LIBDIR=/usr/lib
++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
 +
  #-----Lexer and Parser section-------------------------------------------#
  
@@ -127,7 +127,7 @@ diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004
  ##
  ##########################################################################
  
-+LIBDIR=/usr/lib
++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
 +
  #-----Lexer and Parser section-------------------------------------------#
  
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
new file mode 100644
index 000000000000..74c976e00fd8
--- /dev/null
+++ b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild,v 1.1 2010/06/15 14:45:45 jlec Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs multilib prefix
+
+MY_P="${PN}-v${PV}-prod-src"
+
+DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
+HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
+
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="!<app-text/html-xml-utils-5.3"
+DEPEND="${RDEPEND}
+	>=sci-libs/cifparse-obj-7.025"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-cflags-install.patch
+	epatch "${FILESDIR}"/${P}-gcc-4.3.patch
+	epatch "${FILESDIR}"/${P}-Makefile.patch
+	epatch "${FILESDIR}"/${P}-env.patch
+
+	sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \
+		pdb-extract-v3.0/Makefile \
+		|| die "Failed to fix libdir"
+
+	# Get rid of unneeded directories, to make sure we use system files
+	ebegin "Deleting redundant directories"
+	rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
+		misclib-v2.2 regex-v2.2 tables-v8.0
+	eend
+
+	sed -i \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
+		-e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		"${S}"/etc/make.* \
+		|| die "Failed to fix makefiles"
+
+	eprefixify pdb-extract-v3.0/Makefile etc/*
+}
+
+src_install() {
+	exeinto /usr/libexec/ccp4/bin
+	doexe bin/pdb_extract{,_sf} bin/extract \
+		|| die "failed to install binaries"
+	insinto /usr/include/rcsb
+	doins include/* || die "failed to install include files"
+	dodoc README* || die "failed to install docs"
+	insinto /usr/share/rcsb/
+	doins -r pdb-extract-data || die "failed to install data files"
+
+	cat >> "${T}"/envd <<- EOF
+	PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
+	PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
+	EOF
+
+	newenvd "${T}"/envd 20pdb-extract \
+		|| die "failed to install env files"
+}
diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest
index 545f07203fe0..9f3090b25e26 100644
--- a/sci-chemistry/scala/Manifest
+++ b/sci-chemistry/scala/Manifest
@@ -4,13 +4,13 @@ Hash: SHA1
 AUX Makefile.am 73 RMD160 919c14040b76627428d143027260e9ef2deb2836 SHA1 090d67b6052b322bcc8224b4052bfc9aaf9b0743 SHA256 9b964ac556e8343f4ed45d7293d0144aef569d565141a96a555416aeb411feae
 AUX configure.ac 313 RMD160 098fbafb1f83c2925ff2580c5e0191263b37f574 SHA1 e1550b1b27c967660f7d47c62dea9e693983eca4 SHA256 5c54a92c67fc74f1e4700f53aa9962a0315ec3fb2578c1c13694bfb16d3100ff
 DIST scala-3.3.18.tar.gz 368590 RMD160 e3507d08f4ef435ad1095422c55b80b0297db435 SHA1 5c7baf6c1bd3e40c49a83ca1b4fa5eb76be5a68f SHA256 9c7848289117f5e3f1f83ae3aa18dd958c40a076e13bcb219456bcb9e6055610
-EBUILD scala-3.3.18-r1.ebuild 867 RMD160 547117f840f48b2766c75f46f26981294a513f70 SHA1 0141f21f6e29bd7a9c0c5fd50720526170e1c386 SHA256 4873b773b40d477f18623037399db5d36d92035f428995c8eb6cc21dc1c30e05
-MISC ChangeLog 549 RMD160 7ec93a18f064f62b68f70ea56b9856bc840bacc0 SHA1 9996e248325c3cc62f78967942ce2d1437e18cae SHA256 d2f22d2e2e20f39db20baa0db71bce26e0ee5531b9dd5cbc3763c7bb50e14b37
+EBUILD scala-3.3.18-r1.ebuild 891 RMD160 bd00521260a205a6bc03fae946eb29f5f1a5f147 SHA1 c673ef94a793c15365f68a7a427789e87ea82f7f SHA256 e11281cf255e36d751a23f67f951a554a4625cb91d12d1230f94fbf7632769bd
+MISC ChangeLog 650 RMD160 0d83190110ad368d641069341953fecae96b4ba8 SHA1 c83dabc69e2578ac7e2a101859c665736f9c585e SHA256 ea3c92934d8b823c6183d09b4457b2cd8106e116b3cbf14c62ed0944f0fb679f
 MISC metadata.xml 425 RMD160 21ce42bcdf1513857dd897f43cff75438b3b036d SHA1 26cad89cc010ed1db8965447fa07576239c262f8 SHA256 c6b7700eb561196441fc926c209e3b1503ed82f05403519e6cf7d24ad4612982
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-- 
2.26.2