Added fortran-2.eclass and fix for ifort and pathscale

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

7 files changed, 55 insertions, 176 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 597686978d79..eab43b4cd3f1 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/refmac
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.45 2011/06/14 07:03:57 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.46 2011/06/21 07:55:41 jlec Exp $
+
+  21 Jun 2011; Justin Lecher <jlec@gentoo.org> refmac-5.5.0110-r2.ebuild,
+  refmac-5.5.0110-r3.ebuild, -refmac-5.6.0110.ebuild, -refmac-5.6.0116.ebuild,
+  refmac-5.6.0117.ebuild:
+  Added fortran-2.eclass and fix for ifort and pathscale
 
 *refmac-5.6.0117 (14 Jun 2011)
 
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 95f7f06bbb7b..c0c8c03f183f 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -6,22 +6,18 @@ AUX 5.5.0110-allow-dynamic-linking.patch 2730 RMD160 3637d62986050317a1480e5074e
 AUX 5.5.0110-gcc4.6.patch 473 RMD160 9912c28fec294080ee8e26f27067eaf40317f41d SHA1 e666295b8ddeaa07dc5485660210d001798e46ac SHA256 a33de3aa7236a6b711d5f578fea549da03130eabb061252c40b57e8ce3fe1778
 AUX 5.6.0110-allow-dynamic-linking.patch 16438 RMD160 149cfb8af3f35afc61c26d99d42992f6baa2f265 SHA1 dc5e1b2a95311b043afbd0de5e2b606ee5d42cf8 SHA256 ac854d5e755b05809d4015763b6ea8552f1733d5bc5073778ce82c812083624b
 AUX 5.6.0116-allow-dynamic-linking.patch 16438 RMD160 149cfb8af3f35afc61c26d99d42992f6baa2f265 SHA1 dc5e1b2a95311b043afbd0de5e2b606ee5d42cf8 SHA256 ac854d5e755b05809d4015763b6ea8552f1733d5bc5073778ce82c812083624b
-DIST refmac5.6_source_v5.6.0110.tar.gz 1395208 RMD160 7d29ac54bc2178f0e47e0164f49a8d1567fa44f6 SHA1 6a7abe0190e8f6c74241934f98655b16678cad38 SHA256 5e16f95f374a8df2698644bc334b58474dacc418728542f00ce59d3fa47fbc34
-DIST refmac5.6_source_v5.6.0116.tar.gz 1397818 RMD160 2231e343cf103a4f6b10b9ded1d94626ea27c661 SHA1 daee72506fc67e2a572f4b8134e596df09fdc404 SHA256 c328ad373d3e41c2bd3c0a3343645859020dc008b2f7d071b24c55fe9e182b0d
 DIST refmac5.6_source_v5.6.0117.tar.gz 1291407 RMD160 690beb9ba7ffa59ca4326f91c7ab8ff58b1b3a4c SHA1 9dea92fb08230538d0c1ef14e84383666905a03f SHA256 17a0a63d7d9307a2694e5f3e09d8c4d99b47cbe57ef55ba7cbe16cb2b7fd3590
 DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d497560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca
 DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
-EBUILD refmac-5.5.0110-r2.ebuild 1898 RMD160 46f0bde7cea857a1bf9b8fb1d55508b73679b6a1 SHA1 cf48c4c896c3794dae1d1f4cd9935e0abd1678ee SHA256 35d18396fce6d6154b7cac8edf0825da4640b23ed5e5c208c4da1d6ef3731048
-EBUILD refmac-5.5.0110-r3.ebuild 1991 RMD160 22e48508aba0b15b1a2c97117cfac4e0bc23fab3 SHA1 de0b81e00e2a154af1e4c3d5408307deadaa1076 SHA256 92706139f0b6ab3efbb29a723e965ef8d5551a8a0ab3cdaec65bfdda06502477
-EBUILD refmac-5.6.0110.ebuild 1952 RMD160 7b940afc499b019385f2525228c3f1085239f52d SHA1 93f2233c8ae19db2228a762901259ebd00f52afc SHA256 6e944158ee8f96965053b93b47f0560d740aac02ebadb6c59893080210cbc301
-EBUILD refmac-5.6.0116.ebuild 1951 RMD160 aafd41a425939d485ebcf73663ace016f1ea99ac SHA1 0a93fb7e6b12fb3c481dccf907e4d9045701d914 SHA256 06b1c637c3404ff565eea5282ec8051e64b265f8bc98c9d49fe628a62e606e33
-EBUILD refmac-5.6.0117.ebuild 1954 RMD160 a963000edb99d9f2f5918cf9b53b09ab867b3254 SHA1 22e1241b5b00246fe7f27accd54e917dcd46ed10 SHA256 a62050eeae85a79732e4cf6992931946c69d78fb198dce5b4831b058f4944e9f
-MISC ChangeLog 9008 RMD160 f3b9bdae36079fb3f90dbd9ac9557911e3118144 SHA1 bed08ec097ee9e962b0a3a6a3b4cbfc5e3a366f9 SHA256 11a68a1e616829ec54048fd448ac457b04c9805ec4daf296d2c2348f5257a51d
+EBUILD refmac-5.5.0110-r2.ebuild 2175 RMD160 39306d3920cc876ffd6cfb82fb07ded70fefd384 SHA1 fb09e5ad84060399795ee91dabbd1e25a8e68dbe SHA256 ee667a419b4e4fabe5d61840a8cef367c2c8501dc81914eb908bc840e4b5b80b
+EBUILD refmac-5.5.0110-r3.ebuild 2268 RMD160 2065cbd680e3bf332b6d0241f252905208b439a2 SHA1 87d49e3ed3c13ec698b0d2ac2373097b083f6b72 SHA256 c153a9c9dda0f71a4191ebbcf551dbc783f5456ca291f4c117666b944060a1db
+EBUILD refmac-5.6.0117.ebuild 2230 RMD160 ef31a7f6371619e67c2ab7334e1c5252c5fbab16 SHA1 b9dda036310f51d4a6ea6936a55e7a8364cfc619 SHA256 61b2e9ebc0d73ab2f3d0f169c3c01403965e76a4842f2b993e2501aa0f5e302a
+MISC ChangeLog 9245 RMD160 e3a8cee6552a62fc68fc796e0036829ffbcd317e SHA1 8e114b860718307d6234f0128131e6807d631e48 SHA256 cdd6a4b8b85b507bc923d0622092134d006ce35a27766fa598d1fa617c565b1e
 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
 -----BEGIN PGP SIGNATURE-----
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-VlYAoNHEoFNrJ4ItYouJprIm3VJiCc9z
-=zvsx
+iEYEARECAAYFAk4AToMACgkQgAnW8HDreRZ5/gCfVbX/QiYsq/Y4Xe3pFtf+NiJ2
+4nwAoMOEfxNjJn+gQBztWm1hjxHhcpAI
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diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild
index 70a7ca889896..63dfcb3449f5 100644
--- a/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild,v 1.10 2011/04/21 07:08:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild,v 1.11 2011/06/21 07:55:41 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
-inherit base toolchain-funcs versionator
+inherit base fortran-2 flag-o-matic toolchain-funcs versionator
 
 DESCRIPTION="Macromolecular crystallographic refinement program"
 HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
@@ -25,6 +25,7 @@ RDEPEND="
 	virtual/blas
 	virtual/lapack"
 DEPEND="${RDEPEND}"
+FORTRAN_STANDARD="77 90"
 
 S="${WORKDIR}"
 
@@ -35,6 +36,12 @@ PATCHES=(
 src_prepare() {
 	base_src_prepare
 	use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch
+	[[ ${FC} == *gfortran* ]] && \
+		append-fflags -fno-second-underscore && \
+		append-cflags -DGFORTRAN -DPROTOTYPE && \
+		append-libs -lgfortran -lgfortranbegin -lstdc++
+	[[ ${FC} == *ifort* ]] && \
+		append-libs -lstdc++
 }
 
 src_compile() {
@@ -45,9 +52,11 @@ src_compile() {
 		COPTIM="${CFLAGS}" \
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
-		XFFLAGS="-fno-second-underscore" \
-		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
+		XFFLAGS="" \
+		XCFLAGS="" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb)" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		LLIBOTHERS="${LIBS}" \
 		${PN} libcheck || die
 }
 
diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
index 285a12ebfdf4..5607c018559e 100644
--- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild,v 1.2 2011/04/21 07:08:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild,v 1.3 2011/06/21 07:55:41 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
-inherit base toolchain-funcs versionator
+inherit base fortran-2 flag-o-matic toolchain-funcs versionator
 
 DESCRIPTION="Macromolecular crystallographic refinement program"
 HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
@@ -25,6 +25,7 @@ RDEPEND="
 	virtual/blas
 	virtual/lapack"
 DEPEND="${RDEPEND}"
+FORTRAN_STANDARD="77 90"
 
 S="${WORKDIR}"
 
@@ -36,6 +37,12 @@ PATCHES=(
 src_prepare() {
 	base_src_prepare
 	use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch
+	[[ ${FC} == *gfortran* ]] && \
+		append-fflags -fno-second-underscore && \
+		append-cflags -DGFORTRAN -DPROTOTYPE && \
+		append-libs -lgfortran -lgfortranbegin -lstdc++
+	[[ ${FC} == *ifort* ]] && \
+		append-libs -lstdc++
 }
 
 src_compile() {
@@ -46,9 +53,11 @@ src_compile() {
 		COPTIM="${CFLAGS}" \
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
-		XFFLAGS="-fno-second-underscore" \
-		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
+		XFFLAGS="" \
+		XCFLAGS="" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb)" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		LLIBOTHERS="${LIBS}" \
 		${PN} libcheck || die
 }
 
diff --git a/sci-chemistry/refmac/refmac-5.6.0110.ebuild b/sci-chemistry/refmac/refmac-5.6.0110.ebuild
deleted file mode 100644
index 63bb36965c7a..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0110.ebuild
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0110.ebuild,v 1.2 2011/04/21 07:08:54 jlec Exp $
-
-EAPI="2"
-
-inherit base toolchain-funcs versionator
-
-MY_PV="$(get_version_component_range 1-2)_source_v${PV}"
-
-DESCRIPTION="Macromolecular crystallographic refinement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
-SRC_URI="
-	${HOMEPAGE}/data/refmac_experimental/${PN}${MY_PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	>sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
-
-	)
-
-src_prepare() {
-	base_src_prepare
-	use test && epatch "${FILESDIR}"/5.5-test.log.patch
-}
-
-src_compile() {
-	emake \
-		FC=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		COPTIM="${CFLAGS}" \
-		FOPTIM="${FFLAGS:- -O2}" \
-		VERSION="" \
-		XFFLAGS="-fno-second-underscore -fwhole-file" \
-		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
-		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
-		|| die
-}
-
-src_test() {
-	einfo "Starting tests ..."
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
-	export CCP4_TEST="${WORKDIR}"/test-framework
-	export CCP4_SCR="${T}"
-	ln -sf refmac "${S}"/refmac5
-	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
-	ccp4-run-thorough-tests -v test_refmac5 || die
-}
-
-src_install() {
-	for i in refmac libcheck FreeTwin header2matr; do
-		exeinto /usr/libexec/ccp4/bin/
-		doexe ${i} || die
-		dosym ../libexec/ccp4/bin/${i} /usr/bin/${i}
-	done
-	dosym refmac /usr/bin/refmac5 || die
-	dosym refmac /usr/libexec/ccp4/bin/refmac5 || die
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0116.ebuild b/sci-chemistry/refmac/refmac-5.6.0116.ebuild
deleted file mode 100644
index e55483c44b75..000000000000
--- a/sci-chemistry/refmac/refmac-5.6.0116.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0116.ebuild,v 1.1 2011/04/21 07:08:54 jlec Exp $
-
-EAPI="2"
-
-inherit base toolchain-funcs versionator
-
-MY_PV="$(get_version_component_range 1-2)_source_v${PV}"
-
-DESCRIPTION="Macromolecular crystallographic refinement program"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac"
-SRC_URI="
-	${HOMEPAGE}/data/refmac_experimental/${PN}${MY_PV}.tar.gz
-	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
-
-SLOT="0"
-LICENSE="ccp4"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-
-RDEPEND="
-	>=sci-libs/ccp4-libs-6.1.3-r7
-	sci-libs/mmdb
-	>sci-libs/monomer-db-1
-	virtual/blas
-	virtual/lapack"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
-	)
-
-src_prepare() {
-	base_src_prepare
-	use test && epatch "${FILESDIR}"/5.5-test.log.patch
-}
-
-src_compile() {
-	emake \
-		FC=$(tc-getFC) \
-		CC=$(tc-getCC) \
-		CXX=$(tc-getCXX) \
-		COPTIM="${CFLAGS}" \
-		FOPTIM="${FFLAGS:- -O2}" \
-		VERSION="" \
-		XFFLAGS="-fno-second-underscore -fwhole-file" \
-		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
-		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
-		|| die
-}
-
-src_test() {
-	einfo "Starting tests ..."
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
-	export CCP4_TEST="${WORKDIR}"/test-framework
-	export CCP4_SCR="${T}"
-	ln -sf refmac "${S}"/refmac5
-	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
-	ccp4-run-thorough-tests -v test_refmac5 || die
-}
-
-src_install() {
-	for i in refmac libcheck FreeTwin header2matr; do
-		exeinto /usr/libexec/ccp4/bin/
-		doexe ${i} || die
-		dosym ../libexec/ccp4/bin/${i} /usr/bin/${i}
-	done
-	dosym refmac /usr/bin/refmac5 || die
-	dosym refmac /usr/libexec/ccp4/bin/refmac5 || die
-}
diff --git a/sci-chemistry/refmac/refmac-5.6.0117.ebuild b/sci-chemistry/refmac/refmac-5.6.0117.ebuild
index c7e607f400e6..ad651144ba96 100644
--- a/sci-chemistry/refmac/refmac-5.6.0117.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0117.ebuild
@@ -1,10 +1,10 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0117.ebuild,v 1.1 2011/06/14 07:03:57 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0117.ebuild,v 1.2 2011/06/21 07:55:41 jlec Exp $
 
-EAPI="2"
+EAPI=2
 
-inherit base toolchain-funcs versionator
+inherit base fortran-2 flag-o-matic toolchain-funcs versionator
 
 MY_PV="$(get_version_component_range 1-2)_source_v${PV}"
 
@@ -26,6 +26,7 @@ RDEPEND="
 	virtual/blas
 	virtual/lapack"
 DEPEND="${RDEPEND}"
+FORTRAN_STANDARD="77 90"
 
 S="${WORKDIR}"
 
@@ -36,6 +37,12 @@ PATCHES=(
 src_prepare() {
 	base_src_prepare
 	use test && epatch "${FILESDIR}"/5.5-test.log.patch
+	[[ ${FC} == *gfortran* ]] && \
+		append-fflags -fno-second-underscore && \
+		append-cflags -DGFORTRAN -DPROTOTYPE && \
+		append-libs -lgfortran -lgfortranbegin -lstdc++
+	[[ ${FC} == *ifort* ]] && \
+		append-libs -lstdc++
 }
 
 src_compile() {
@@ -46,9 +53,11 @@ src_compile() {
 		COPTIM="${CFLAGS}" \
 		FOPTIM="${FFLAGS:- -O2}" \
 		VERSION="" \
-		XFFLAGS="-fno-second-underscore -fwhole-file" \
-		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb) -lstdc++" \
+		XFFLAGS="-fwhole-file" \
+		XCFLAGS="" \
+		LLIBCCP="-lccp4f -lccp4c -lccif $(pkg-config --libs mmdb)" \
 		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		LLIBOTHERS="${LIBS}" \
 		|| die
 }