diff options
Diffstat (limited to 'sci-chemistry/refmac')
-rw-r--r-- | sci-chemistry/refmac/ChangeLog | 9 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.5.0109.ebuild | 68 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.5.0110-r1.ebuild | 69 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild | 13 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.5.0110.ebuild | 70 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0093.ebuild | 71 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0094.ebuild | 71 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0096.ebuild | 71 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0097.ebuild | 9 |
9 files changed, 20 insertions, 431 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index 1f05bf339c6b..b6760626c22b 100644 --- a/sci-chemistry/refmac/ChangeLog +++ b/sci-chemistry/refmac/ChangeLog @@ -1,6 +1,13 @@ # 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 1.32 2011/01/04 08:55:21 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.33 2011/01/10 21:17:34 jlec Exp $ + + 10 Jan 2011; Justin Lecher <jlec@gentoo.org> -refmac-5.5.0109.ebuild, + -refmac-5.5.0110.ebuild, -refmac-5.5.0110-r1.ebuild, + refmac-5.5.0110-r2.ebuild, -refmac-5.6.0093.ebuild, -refmac-5.6.0094.ebuild, + -refmac-5.6.0096.ebuild, refmac-5.6.0097.ebuild: + Moved the installation of profile files from sci-chemistry/ccp4-apps to + sci-libs/ccp4-libs, #349700 *refmac-5.6.0097 (04 Jan 2011) diff --git a/sci-chemistry/refmac/refmac-5.5.0109.ebuild b/sci-chemistry/refmac/refmac-5.5.0109.ebuild deleted file mode 100644 index 7332f0d9dd88..000000000000 --- a/sci-chemistry/refmac/refmac-5.5.0109.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0109.ebuild,v 1.5 2010/12/16 13:56:18 jlec Exp $ - -EAPI="2" - -inherit base toolchain-funcs versionator - -DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" -SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-libs/ccp4-libs - sci-libs/mmdb - <sci-libs/monomer-db-1 - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND}" - -S="${WORKDIR}" - -PATCHES=( - "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-linking.patch - ) - -src_prepare() { - base_src_prepare - use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch -} - -src_compile() { - emake \ - FC=$(tc-getFC) \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - COPTIM="${CFLAGS}" \ - FOPTIM="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="-fno-second-underscore" \ - LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="-llapack -lblas" \ - || die -} - -src_test() { - einfo "Starting tests ..." - 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 makecif; do - dobin ${i} || die - done - dosym refmac /usr/bin/refmac5 || die - dodoc refmac_keywords.pdf bugs_and_features.pdf || die -} diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r1.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r1.ebuild deleted file mode 100644 index bf3ddef06621..000000000000 --- a/sci-chemistry/refmac/refmac-5.5.0110-r1.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2010 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-r1.ebuild,v 1.3 2010/12/16 13:56:18 jlec Exp $ - -EAPI="2" - -inherit base toolchain-funcs versionator - -DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" -SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-chemistry/makecif - sci-libs/ccp4-libs - 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 "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch -} - -src_compile() { - emake \ - FC=$(tc-getFC) \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - COPTIM="${CFLAGS}" \ - FOPTIM="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="-fno-second-underscore" \ - LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="-llapack -lblas" \ - || die -} - -src_test() { - einfo "Starting tests ..." - 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() { - exeinto /usr/libexec/ccp4/bin/ - doexe ${PN} || die - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dosym refmac /usr/bin/refmac5 || die - dodoc refmac_keywords.pdf bugs_and_features.pdf || die -} diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild index ef1841ec6098..0d8ccf9a73a8 100644 --- a/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild +++ b/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild @@ -1,14 +1,15 @@ -# Copyright 1999-2010 Gentoo Foundation +# 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 1.3 2010/12/31 16:08:51 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.5.0110-r2.ebuild,v 1.4 2011/01/10 21:17:34 jlec Exp $ EAPI="2" inherit base toolchain-funcs versionator DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" -SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" +SRC_URI=" + ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" SLOT="0" @@ -18,7 +19,7 @@ IUSE="test" RDEPEND=" sci-chemistry/makecif - >=sci-libs/ccp4-libs-6.1.3-r5 + >=sci-libs/ccp4-libs-6.1.3-r7 sci-libs/mmdb <sci-libs/monomer-db-1 virtual/blas @@ -46,7 +47,7 @@ src_compile() { VERSION="" \ XFFLAGS="-fno-second-underscore" \ LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="-llapack -lblas" \ + LLIBLAPACK="$(pkg-config --libs lapack blas)" \ ${PN} libcheck || die } diff --git a/sci-chemistry/refmac/refmac-5.5.0110.ebuild b/sci-chemistry/refmac/refmac-5.5.0110.ebuild deleted file mode 100644 index 267b8f492ac5..000000000000 --- a/sci-chemistry/refmac/refmac-5.5.0110.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2010 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.ebuild,v 1.4 2010/12/16 13:56:18 jlec Exp $ - -EAPI="2" - -inherit base toolchain-funcs versionator - -DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" -SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-libs/ccp4-libs - 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 "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch -} - -src_compile() { - emake \ - FC=$(tc-getFC) \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - COPTIM="${CFLAGS}" \ - FOPTIM="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="-fno-second-underscore" \ - LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="-llapack -lblas" \ - || die -} - -src_test() { - einfo "Starting tests ..." - 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 makecif; do - exeinto /usr/libexec/ccp4/bin/ - doexe ${i} || die - dosym ../libexec/ccp4/bin/${i} /usr/bin/${i} - done - dosym refmac /usr/bin/refmac5 || die - dodoc refmac_keywords.pdf bugs_and_features.pdf || die -} diff --git a/sci-chemistry/refmac/refmac-5.6.0093.ebuild b/sci-chemistry/refmac/refmac-5.6.0093.ebuild deleted file mode 100644 index 523ded34e934..000000000000 --- a/sci-chemistry/refmac/refmac-5.6.0093.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0093.ebuild,v 1.2 2010/12/16 13:56:18 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}${MY_PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-libs/ccp4-libs - sci-libs/mmdb - >sci-libs/monomer-db-1 - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND}" - -S="${WORKDIR}" - -PATCHES=( - "${FILESDIR}"/5.6.0092-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" \ - LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="$(pkg-config --libs lapack blas)" \ - || die -} - -src_test() { - einfo "Starting tests ..." - export PATH="${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 -} diff --git a/sci-chemistry/refmac/refmac-5.6.0094.ebuild b/sci-chemistry/refmac/refmac-5.6.0094.ebuild deleted file mode 100644 index ce851c416824..000000000000 --- a/sci-chemistry/refmac/refmac-5.6.0094.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0094.ebuild,v 1.2 2010/12/16 13:56:18 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}${MY_PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-libs/ccp4-libs - sci-libs/mmdb - >sci-libs/monomer-db-1 - virtual/blas - virtual/lapack" -DEPEND="${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="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="-fno-second-underscore" \ - LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="$(pkg-config --libs lapack blas)" \ - || die -} - -src_test() { - einfo "Starting tests ..." - 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 -} diff --git a/sci-chemistry/refmac/refmac-5.6.0096.ebuild b/sci-chemistry/refmac/refmac-5.6.0096.ebuild deleted file mode 100644 index bdcebe6324f4..000000000000 --- a/sci-chemistry/refmac/refmac-5.6.0096.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0096.ebuild,v 1.1 2010/12/21 07:39:22 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}${MY_PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-libs/ccp4-libs - sci-libs/mmdb - >sci-libs/monomer-db-1 - virtual/blas - virtual/lapack" -DEPEND="${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="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="-fno-second-underscore" \ - LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ - LLIBLAPACK="$(pkg-config --libs lapack blas)" \ - || die -} - -src_test() { - einfo "Starting tests ..." - 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 -} diff --git a/sci-chemistry/refmac/refmac-5.6.0097.ebuild b/sci-chemistry/refmac/refmac-5.6.0097.ebuild index 44fd3c1415d2..85865ce92844 100644 --- a/sci-chemistry/refmac/refmac-5.6.0097.ebuild +++ b/sci-chemistry/refmac/refmac-5.6.0097.ebuild @@ -1,6 +1,6 @@ # 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-5.6.0097.ebuild,v 1.1 2011/01/04 08:55:21 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0097.ebuild,v 1.2 2011/01/10 21:17:34 jlec Exp $ EAPI="2" @@ -9,8 +9,9 @@ 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 +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" @@ -19,7 +20,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="test" RDEPEND=" - sci-libs/ccp4-libs + >=sci-libs/ccp4-libs-6.1.3-r7 sci-libs/mmdb >sci-libs/monomer-db-1 virtual/blas |