Version Bump, bug #390165, bug #521292; drop old, obsolets bug #478596, bug #552712

Package-Manager: portage-2.2.20/cvs/Linux x86_64
Manifest-Sign-Key: 0xE9402A79B03529A2!

6 files changed, 78 insertions, 113 deletions

diff --git a/sci-chemistry/tinker/ChangeLog b/sci-chemistry/tinker/ChangeLog
index f01236edd2df..bc50f1ca4d99 100644
--- a/sci-chemistry/tinker/ChangeLog
+++ b/sci-chemistry/tinker/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/tinker
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.33 2012/10/19 10:30:49 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/ChangeLog,v 1.34 2015/06/21 10:42:07 jlec Exp $
+
+*tinker-7.1.2 (21 Jun 2015)
+
+  21 Jun 2015; Justin Lecher <jlec@gentoo.org> +files/7.1.2-openmp.patch,
+  +files/tinker-7.1.2-build.patch, +tinker-7.1.2.ebuild, -tinker-5.1.09.ebuild,
+  -tinker-6.ebuild:
+  Version Bump, bug #390165, bug #521292; drop old, obsolets bug #478596, bug
+  #552712
 
   19 Oct 2012; Justin Lecher <jlec@gentoo.org> tinker-5.1.09.ebuild,
   tinker-6.ebuild, metadata.xml:
@@ -146,4 +154,3 @@
   +tinker-4.2.ebuild:
   (#35945) New molecular mechanics package. Heavily modified ebuild based on
   that of Jeremy Warren <jwarren@cheesefoam.dyndns.org>.
-
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
index cc1c08103915..cf5a89376676 100644
--- a/sci-chemistry/tinker/Manifest
+++ b/sci-chemistry/tinker/Manifest
@@ -1,19 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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-DIST tinker-5.1.09.tar.gz 14071638 SHA256 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183
-DIST tinker-6.tar.gz 18475753 SHA256 f3962cf39df1ccfb2a425837add7de58cda3e21adebbe1141fee6e3869ba5fc0
-EBUILD tinker-5.1.09.ebuild 1901 SHA256 7e33fce276737ae5252584039ec3c84e369bdc3114d1c39b386b129e59f03ccc SHA512 8190d03d4aae6e2e1250109e84667064b1ac0451979175f401b78829282a2d6232465beee01a002444e8f253727d01c0e7522c3bd7f6c86e05e0cd6472e7e069 WHIRLPOOL 47733e1903e4681c9e4829b1f34343a681f774f305857c85e9af0e1f7bd583d0b7a5f7ac68453809b2b4f591d0dfb7a4be8877a3225a92e92a11ab3a89870e0c
-EBUILD tinker-6.ebuild 2419 SHA256 6f786bf812dfc0d13aa40ae9794ddd60a4b86063c51971a0f5f89e123aaceb13 SHA512 05567a1af6b298983ee3e9b34b7b18a066ff2ad79840787b5c2c9b6449d81479014542e5e0e5a713619f355bbbc5111a9afc3ce95f4f04de31db63e4a075b1dc WHIRLPOOL 086429d266450e97e0831fa8e125ef972b35409e1371c6fef3a92eab76c397805f987d45412d90da9f17295aefec6a5f141a4068d26a5beee16b4d31837cb902
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+AUX 7.1.2-openmp.patch 400 SHA256 67cf53b3801814ab39b4bdbb40db9f500cbc4740e2b7db94a945829ef1961cec SHA512 1af405acc753d602501589725374e88964a55e5954cb77eb1f3c0156fa73936552be9ce5fc4f36c855dfbd4043f12749dfc95aa9b946d80d0e5e6e8100e84ad4 WHIRLPOOL 6f20e980f63f79d3443f46d5608ad241723b73026cc3ec85437cb741a1c2b7b3fe74de428097583f3f34ac05d85e14edfe0490a04d48cccfd64d4ded2850dfb2
+AUX tinker-7.1.2-build.patch 360 SHA256 26fba46b9a72407cfd194cf74d5044b06b41164ae039b0b97f29b1840be4f765 SHA512 b20a4d8e75a781cd9c769dd0b5ae4e1039ea54d7ac61fc3605543b796afa2f4f3957be439f338fd47090a17e9153a466c2f76b364f4d9b7a2705b746f6cefbd3 WHIRLPOOL e102e8fafacc51160e191535355ae6fc7216c76b21234f6878c252eeebcb306bac8678413da26b44ff20a32b7652eda189eb66eb44efd577eb007e8685f8222f
+DIST tinker-7.1.2.tar.gz 28468683 SHA256 fdee18915cff9044fd083bb2271083c221db6d05de2cb98fc111b136e23e6899 SHA512 4524259754b0f11d7e2e8997ebd85eae7d28f8dbb1edb2d9818aa0a96640de0049aa4937236694f1a11743dee187d612f775b233a73cc96c2708d620457a7dc2 WHIRLPOOL f3e29eaf67d25ae6d4f3c4e3546798e66bd626929fddd45b9d1ff9f2143cd57dcc5079226f3ceaa142f4c6a168c4a150a51be1336a5ca13384338795ef3a6d46
+EBUILD tinker-7.1.2.ebuild 2372 SHA256 b2fea820b25954304edfb92786dd48ef56a4794dc866bda76839bbc5cdcf9706 SHA512 f43bd926b8d8e9437400e0cbb4e23ed4bf2e869909319453994aafeec007f07e2dfaad439f16514f87240c91ba692b39ea9ca57a44881b8d253afb04a3826c93 WHIRLPOOL 74d467f2666cedd97b3fd074b6c578f8e35bc24b4079bebb1a605e6cc583f49891d06ced4a9979559e7c461f70792fb59874947ab2c2c249a81ad74dbe715294
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diff --git a/sci-chemistry/tinker/files/7.1.2-openmp.patch b/sci-chemistry/tinker/files/7.1.2-openmp.patch
new file mode 100644
index 000000000000..f3e8e2932b4a
--- /dev/null
+++ b/sci-chemistry/tinker/files/7.1.2-openmp.patch
@@ -0,0 +1,15 @@
+diff --git a/source/initial.f b/source/initial.f
+index 835f228..4099c74 100644
+--- a/source/initial.f
++++ b/source/initial.f
+@@ -73,8 +73,8 @@ c
+ c
+ c     Intel compiler extensions to OpenMP standard
+ c
+-!$    call kmp_set_stacksize_s (2**28)
+-!$    call kmp_set_blocktime (0)
++!    call kmp_set_stacksize_s (2**28)
++!    call kmp_set_blocktime (0)
+ c
+ c     values of machine precision constants
+ c
diff --git a/sci-chemistry/tinker/files/tinker-7.1.2-build.patch b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch
new file mode 100644
index 000000000000..d6ef484b19a4
--- /dev/null
+++ b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch
@@ -0,0 +1,17 @@
+ make/Makefile | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/make/Makefile b/make/Makefile
+index 61d5037..9be384a 100644
+--- a/make/Makefile
++++ b/make/Makefile
+@@ -719,8 +719,7 @@ EXEFILES = alchemy.x \
+ %.x: %.o libtinker.a
+ 	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
+ 
+-all:
+-	${EXEFILES}
++all: ${EXEFILES}
+ 
+ install:
+ 	rename
diff --git a/sci-chemistry/tinker/tinker-5.1.09.ebuild b/sci-chemistry/tinker/tinker-5.1.09.ebuild
deleted file mode 100644
index bad799754325..000000000000
--- a/sci-chemistry/tinker/tinker-5.1.09.ebuild
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-5.1.09.ebuild,v 1.7 2012/10/19 10:30:49 jlec Exp $
-
-EAPI="2"
-
-inherit eutils fortran-2 java-pkg-opt-2 toolchain-funcs
-
-DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM"
-HOMEPAGE="http://dasher.wustl.edu/tinker/"
-SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="Tinker"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-DEPEND="
-	>=virtual/jdk-1.6"
-RDEPEND="
-	dev-libs/maloc
-	!dev-util/diffuse
-	>=virtual/jre-1.6"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/tinker/source
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	java-pkg-opt-2_pkg_setup
-}
-
-src_prepare() {
-	cd ..
-	epatch "${FILESDIR}"/${PV}-Makefile.patch
-}
-
-src_compile() {
-	local javalib=
-	for i in $(java-config -g LDPATH | sed 's|:| |g'); do
-		[[ -f ${i}/libjvm.so ]] && javalib=${i}
-	done
-	emake -e \
-		-f ../make/Makefile \
-		F77="$(tc-getFC)" \
-		CC="$(tc-getCC) -c" \
-		F77FLAGS=-c \
-		OPTFLAGS="${FFLAGS}" \
-		LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \
-		INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \
-		LIBS=" -lmaloc -L${javalib} -ljvm" \
-		all || die
-	mkdir "${S}"/../bin || die
-
-	emake \
-		-f ../make/Makefile \
-		BINDIR="${S}"/../bin \
-		rename || die
-}
-
-src_test() {
-	cd "${WORKDIR}"/tinker/test/
-	for test in *.run; do
-		einfo "Testing ${test} ..."
-		bash ${test} || die
-	done
-}
-
-src_install() {
-	dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* || die
-
-	insinto /usr/share/${PN}/
-	doins -r "${WORKDIR}"/${PN}/params || die
-
-	dodoc \
-		"${WORKDIR}"/${PN}/doc/{*.txt,announce/release-*,*.pdf,0README} || die
-
-	if use examples; then
-		insinto /usr/share/${P}
-		doins -r "${WORKDIR}"/${PN}/example || die
-
-		doins -r "${WORKDIR}"/${PN}/test || die
-	fi
-
-}
diff --git a/sci-chemistry/tinker/tinker-6.ebuild b/sci-chemistry/tinker/tinker-7.1.2.ebuild
index 3fd9619c811e..0fe97c213b86 100644
--- a/sci-chemistry/tinker/tinker-6.ebuild
+++ b/sci-chemistry/tinker/tinker-7.1.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-6.ebuild,v 1.6 2012/10/19 10:30:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/tinker/tinker-7.1.2.ebuild,v 1.1 2015/06/21 10:42:07 jlec Exp $
 
-EAPI=2
+EAPI=5
 
 inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs
 
@@ -25,7 +25,7 @@ RDEPEND="
 
 RESTRICT="mirror"
 
-S="${WORKDIR}"/${PN}${PV}/source
+S="${WORKDIR}"/${PN}/source
 
 pkg_setup() {
 	fortran-2_pkg_setup
@@ -36,6 +36,7 @@ pkg_setup() {
 src_prepare() {
 	sed 's:strip:true:g' -i ../make/Makefile
 	[[ $(tc-getFC) =~ "ifort" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch
+	cd .. && epatch "${FILESDIR}"/${P}-build.patch
 }
 
 src_compile() {
@@ -55,7 +56,7 @@ src_compile() {
 		_omplib="-liomp5"
 	fi
 
-	_fftwlib="$(pkg-config --libs fftw3 fftw3_threads)"
+	_fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)"
 
 	emake \
 		-f ../make/Makefile \
@@ -66,18 +67,18 @@ src_compile() {
 		LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \
 		INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \
 		LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \
-		all || die
+		all
 
 	mkdir "${S}"/../bin || die
 
 	emake \
 		-f ../make/Makefile \
 		BINDIR="${S}"/../bin \
-		rename || die
+		rename
 }
 
 src_test() {
-	cd "${WORKDIR}"/${PN}${PV}/test/
+	cd "${WORKDIR}"/${PN}/test/
 	for test in *.run; do
 		einfo "Testing ${test} ..."
 		bash ${test} || die
@@ -85,19 +86,19 @@ src_test() {
 }
 
 src_install() {
-	dobin "${WORKDIR}"/${PN}${PV}/perl/mdavg "${WORKDIR}"/${PN}${PV}/bin/* || die
+	dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/*
 
 	insinto /usr/share/${PN}/
-	doins -r "${WORKDIR}"/${PN}${PV}/params || die
+	doins -r "${WORKDIR}"/${PN}/params
 
 	dodoc \
-		"${WORKDIR}"/${PN}${PV}/doc/{*.txt,announce/release-*,*.pdf,0README} || die
+		"${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README}
 
 	if use examples; then
 		insinto /usr/share/${P}
-		doins -r "${WORKDIR}"/${PN}${PV}/example || die
+		doins -r "${WORKDIR}"/${PN}/example
 
-		doins -r "${WORKDIR}"/${PN}${PV}/test || die
+		doins -r "${WORKDIR}"/${PN}/test
 	fi
 
 }