diff options
| author |   Aaron Bauman <bman@gentoo.org> | 2019-11-20 12:09:50 -0500 |
|---|---|---|
| committer | Aaron Bauman <bman@gentoo.org> | 2019-11-20 12:27:41 -0500 |
| commit | a9bfbe13e106ddc647bbd6d8f94ea4b65b50d3a5 (patch) | |
| tree | d9db36c6c83001b2346e344300607e738958d4fb /sci-chemistry | |
| parent | app-i18n/scim-wnn: drop last-rited packages (diff) | |
| download | gentoo-a9bfbe13e106ddc647bbd6d8f94ea4b65b50d3a5.tar.gz gentoo-a9bfbe13e106ddc647bbd6d8f94ea4b65b50d3a5.tar.bz2 gentoo-a9bfbe13e106ddc647bbd6d8f94ea4b65b50d3a5.zip | |
sci-chemistry{,libs}/*: drop last-rited packages
Signed-off-by: Aaron Bauman <bman@gentoo.org>
Diffstat (limited to 'sci-chemistry')
33 files changed, 0 insertions, 2309 deletions
diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest deleted file mode 100644 index 9776d3f8382e..000000000000 --- a/sci-chemistry/aria/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST aria2.3.2_08.26.2013.tar.gz 1878602 BLAKE2B 3044192853c0ed0653d20fea959d3b01321f559845c555289658f93b65e9148f8cd0f59619e8690887b2811d613e6cc2f67b67af7d84ade4b8fc18403367086c SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e diff --git a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild deleted file mode 100644 index c06c8d979bb6..000000000000 --- a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild +++ /dev/null @@ -1,88 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit eutils python-single-r1 versionator - -MY_P="${PN}$(get_version_component_range 1-2 ${PV})" -DATE="08.26.2013" - -DESCRIPTION="Automated NOE assignment and NMR structure calculation" -HOMEPAGE="http://aria.pasteur.fr/" -SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2_${DATE}.tar.gz" - -SLOT="0" -LICENSE="cns" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-tcltk/tix - dev-lang/tk:0= - >=dev-python/numpy-1.1[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP},tk] - >=sci-chemistry/cns-1.2.1-r7[aria,openmp] - >=sci-chemistry/ccpn-2.2[${PYTHON_USEDEP}] - sci-chemistry/clashlist - sci-chemistry/procheck - sci-libs/clashscore-db" -DEPEND="${RDEPEND}" - -RESTRICT="fetch" - -S="${WORKDIR}/${MY_P}" - -pkg_nofetch(){ - einfo "Go to http://aria.pasteur.fr/archives/aria2.3.2.tar.gz/view, download ${A}" - einfo "and place it into your DISTDIR directory." -} - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_test(){ - export CCPNMR_TOP_DIR=$(python_get_sitedir) - export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python - ${PYTHON} check.py || die -} - -src_install(){ - python_moduleinto ${PN} - python_domodule src aria2.py - python_moduleinto ${PN}/cns - python_domodule cns/{protocols,toppar,src/helplib} - - if use examples; then - insinto /usr/share/${P}/ - doins -r examples - fi - - # ENV - cat >> "${T}"/20aria <<- EOF - ARIA2="$(python_get_sitedir)/${PN}" - EOF - - doenvd "${T}"/20aria - - # Launch Wrapper - cat >> "${T}"/aria <<- EOF - #!/bin/sh - export CCPNMR_TOP_DIR="$(python_get_sitedir)" - export PYTHONPATH="$(python_get_sitedir)/ccpn/python" - exec "${PYTHON}" -O "\${ARIA2}"/aria2.py \$@ - EOF - - dobin "${T}"/aria - dosym aria /usr/bin/aria2 - - dodoc README - python_optimize "${D}/$(python_get_sitedir)" -} diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/aria/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest deleted file mode 100644 index 1c3150073f0f..000000000000 --- a/sci-chemistry/ccpn/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -DIST analysis2.4.1.tar.gz 36088236 BLAKE2B 8aaf4ffe5a8dc7a6b805a7a66e163cb03b0fc8a45617ebf892268a2f3658e49c48e3c2de4ea654a840eef2c01cf3a3f28f45e053697e68bbc83ce22d19a29cf3 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 -DIST analysis2.4.2.tar.gz 36390919 BLAKE2B 5e7fa44b2029d834ef634b2cd9f2c34d7e6dbfd3e257b9344cff92d13750a21325a2a2f82eb072ae385c528a7406796959c8201edbc1422bc54a17e176d7db33 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b -DIST ccpn-update-2.4.1-150226.patch.xz 10732 BLAKE2B 9f31bd16e7a866b016c5db8b837e3ee926d2db7cd3b15e7cd32fe00f7723e511214d36221ba86651e79223f0a1d30e2402aa446eb063a078b989102032ae743b SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb -DIST ccpn-update-2.4.2-150325.patch.xz 2096 BLAKE2B 589c8129d2e1df6231412cd1398823208cbdc7307f63f3a5480a65e428aeb0b6411b9110ddd380ad37addd2ea9118bc6156662c5fd80a7eee362f53fd417e724 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 -DIST ccpn-update-2.4.2-150413.patch.xz 3132 BLAKE2B f4d55e4b301df4500f29d281de2b274f7912d61d1ad54fedf992e76dd254e86dcb2e9d2a2f4d58ce028d4c9df6bedad847a9e72bef7627800c2d31cc7c43909e SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d -DIST ccpn-update-2.4.2-150421.patch.xz 3788 BLAKE2B 125eed69e2593e0ab64e6d3cdcee026c4af067c3aa2e9742b033741cc65cc0391fb86c825b372c02dcd549ca260196fd4e8938516d218653d3db80f60ce9caf2 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648 diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild deleted file mode 100644 index 6303b8d42837..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -#PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild deleted file mode 100644 index a1755eca7d7d..000000000000 --- a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="ssl,tk" - -inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator - -PATCHSET="${PV##*_p}" -MY_PN="${PN}mr" -MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" -MY_MAJOR="$(get_version_component_range 1-3)" - -DESCRIPTION="The Collaborative Computing Project for NMR" -HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" -SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" -[[ -n ${PATCHSET} ]] \ - && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" - -SLOT="0" -LICENSE="|| ( CCPN LGPL-2.1 )" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+opengl" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-lang/tk:0=[threads] - dev-python/numpy[${PYTHON_USEDEP}] - dev-tcltk/tix - =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] - sci-biology/psipred - x11-libs/libXext - x11-libs/libX11 - opengl? ( - media-libs/freeglut - dev-python/pyglet[${PYTHON_USEDEP}] - )" -DEPEND="${RDEPEND}" - -RESTRICT="mirror" - -S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) - -src_prepare() { - [[ -n ${PATCHSET} ]] && \ - EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch - - epatch "${FILESDIR}"/2.3.1-parallel.patch - - append-lfs-flags - - sed \ - -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ - -e "s:weights_s:weights:g" \ - -i python/ccpnmr/analysis/wrappers/Psipred.py || die - - local tk_ver - local myconf - - tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" - - if use opengl; then - GLUT_NEED_INIT="-DNEED_GLUT_INIT" - IGNORE_GL_FLAG="" - GL_FLAG="-DUSE_GL_TRUE" - GL_DIR="${EPREFIX}/usr" - GL_LIB="-lglut -lGLU -lGL" - GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" - GL_LIB_FLAGS="" - else - IGNORE_GL_FLAG="-DIGNORE_GL" - GL_FLAG="-DUSE_GL_FALSE" - fi - - GLUT_NOT_IN_GL="" - GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" - - rm -rf data model doc license || die - - sed \ - -e "s|/usr|${EPREFIX}/usr|g" \ - -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ - -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ - -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ - -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ - -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ - -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ - -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ - -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ - -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ - -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ - -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ - -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ - -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ - -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ - -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ - c/environment_default.txt > c/environment.txt || die - - sed \ - -e 's:ln -s:cp -f:g' \ - -i $(find python -name linkSharedObjs) || die -} - -src_compile() { - emake -C c all - emake -C c links -} - -src_install() { - local libdir - local tkver - local _wrapper - - find . -name "*.pyc" -type f -delete || die - - libdir=$(get_libdir) - tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) - - _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" - for wrapper in ${_wrapper}; do - sed \ - -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|${EPYTHON}|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ - "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" - dobin "${T}"/${wrapper} - done - - local in_path=$(python_get_sitedir)/${PN} - local files - local pydocs - - pydocs="$(find python -name doc -type d)" - rm -rf ${pydocs} || die - - for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do - sed \ - -e 's|#from __future__|from __future__|g' \ - -i ${i} || die - done - - dodir ${in_path#${EPREFIX}}/c - - ebegin "Installing main files" - python_moduleinto ${PN} - python_domodule python - eend - - ebegin "Adjusting permissions" - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done - eend - python_optimize -} diff --git a/sci-chemistry/ccpn/files/2.3.1-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch deleted file mode 100644 index fcf44707e082..000000000000 --- a/sci-chemistry/ccpn/files/2.3.1-parallel.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/ccpnmr2.3/c/Makefile b/ccpnmr2.3/c/Makefile -index 01fb25a..8e8e1fe 100644 ---- a/ccpnmr2.3/c/Makefile -+++ b/ccpnmr2.3/c/Makefile -@@ -5,22 +5,22 @@ all: compile - compile: global structure analysis clouds dynamics bayes - - global: -- cd memops/global && $(MAKE) -+ $(MAKE) -C memops/global - --structure: -- cd ccp/structure && $(MAKE) -+structure: global -+ $(MAKE) -C ccp/structure - --analysis: -- cd ccpnmr/analysis && $(MAKE) -+analysis: global -+ $(MAKE) -C ccpnmr/analysis - --clouds: -- cd ccpnmr/clouds && $(MAKE) -+clouds: global -+ $(MAKE) -C ccpnmr/clouds - --dynamics: -- cd ccpnmr/dynamics && $(MAKE) -+dynamics: global -+ $(MAKE) -C ccpnmr/dynamics - --bayes: -- cd other/cambridge/bayes && $(MAKE) -+bayes: global -+ $(MAKE) -C other/cambridge/bayes - - clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean - diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis deleted file mode 100644 index 828ed4e64ae9..000000000000 --- a/sci-chemistry/ccpn/files/analysis +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle deleted file mode 100644 index 6d8a42e615de..000000000000 --- a/sci-chemistry/ccpn/files/dangle +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter deleted file mode 100644 index c083960f2f60..000000000000 --- a/sci-chemistry/ccpn/files/dataShifter +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter deleted file mode 100644 index 09505ccc4925..000000000000 --- a/sci-chemistry/ccpn/files/depositionFileImporter +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@ diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci deleted file mode 100644 index 54d913348718..000000000000 --- a/sci-chemistry/ccpn/files/eci +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $* diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr deleted file mode 100644 index a2fe4c997c7c..000000000000 --- a/sci-chemistry/ccpn/files/extendNmr +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@ diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter deleted file mode 100644 index 6cb273612352..000000000000 --- a/sci-chemistry/ccpn/files/formatConverter +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara deleted file mode 100644 index 5a3710a134a7..000000000000 --- a/sci-chemistry/ccpn/files/pipe2azara +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara deleted file mode 100644 index 7b73714c2fa5..000000000000 --- a/sci-chemistry/ccpn/files/xeasy2azara +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python -export TCL_LIBRARY=gentootcl -export TK_LIBRARY=gentootk -export PSIPRED_DIR=gentoousr -gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-chemistry/ccpn/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest deleted file mode 100644 index 34efe8e5f559..000000000000 --- a/sci-chemistry/cns/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST aria2.3.1.tar.gz 1833973 BLAKE2B 4bf51626a4283452e75a834d0160a4204efd5a35ee8b07329f2a4f933ceea23e53177e6ed19bc9cc158b2a00491d20c75d443bdc04e7feb2d7eda3dc006818e1 SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5 -DIST aria2.3.2.tar.gz 1836270 BLAKE2B 725b0db2b5de36d1b132c5073b8a91f26fa19b48549f4c899041a2b140127524f660c4faeb8c35e94d3d19c24b0252f379de0e85c8fb08b86fc7834252239fb9 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa -DIST cns_solve_1.21_all-mp.tar.gz 32748040 BLAKE2B 7c82fd9cddc56a00d791d6d5525491b91525962f000c2fdfb02a3ab81305c0c026c115c2328dac99ac7b30146ca591620f4f42019938fb49e7ce52235b281121 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857 -DIST cns_solve_1.3_all.tar.gz 64167735 BLAKE2B 3901a597eb0deac7f2fad173e15d78bfcd753c4019739e22c8851194c9446305cd92bcff73f7f06dc21b6d055852863993412296e1e555ef0b3b730052934cbd SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37 diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild deleted file mode 100644 index c9d9a80f36af..000000000000 --- a/sci-chemistry/cns/cns-1.2.1-r8.ebuild +++ /dev/null @@ -1,232 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic - -MY_PN="${PN}_solve" -MY_PV="$(delete_version_separator 2)" -MY_P="${MY_PN}_${MY_PV}" - -DESCRIPTION="Crystallography and NMR System" -HOMEPAGE="http://cns.csb.yale.edu/" -SRC_URI=" - ${MY_P}_all-mp.tar.gz - aria? ( aria2.3.2.tar.gz )" - -SLOT="0" -LICENSE="cns" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="aria openmp" - -RDEPEND="app-shells/tcsh" -DEPEND="${RDEPEND}" - -FORTRAN_NEED_OPENMP=1 - -S="${WORKDIR}/${MY_P}" - -RESTRICT="fetch test" - -pkg_nofetch() { - elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" - use aria && elog "and http://aria.pasteur.fr/" - elog "and place these files:" - elog ${A} - elog "into your DISTDIR directory." -} - -get_fcomp() { - case $(tc-getFC) in - *gfortran* ) - FCOMP="gfortran" ;; - ifort ) - FCOMP="ifc" ;; - * ) - FCOMP=$(tc-getFC) ;; - esac -} - -pkg_setup() { - fortran-2_pkg_setup - get_fcomp -} - -get_bitness() { - echo > "${T}"/test.c - $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o - case $(file "${T}"/test.o) in - *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; - *32-bit*|*ppc*|*i386*) export _bitness="32";; - *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; - esac -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-gentoo.patch \ - "${FILESDIR}"/${PV}-parallel.patch - - get_bitness - - if use aria; then - pushd "${WORKDIR}"/aria* >& /dev/null - # Update the cns sources in aria for version 1.2.1 - epatch "${FILESDIR}"/1.2.1-aria2.3.patch - - # Update the code with aria specific things - cp -rf cns/src/* "${S}"/source/ || die - popd >& /dev/null - fi - - # the code uses Intel-compiler-specific directives - if [[ $(tc-getFC) =~ gfortran ]]; then - epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch - use openmp && \ - append-flags -fopenmp && append-ldflags -fopenmp - COMP="gfortran" - [[ ${_bitness} == 64 ]] && \ - append-fflags -fdefault-integer-8 - elif [[ $(tc-getFC) == if* ]]; then - epatch "${FILESDIR}"/${PV}-ifort.patch - use openmp && \ - append-flags -openmp && append-ldflags -openmp - COMP="ifort" - [[ ${_bitness} == 64 ]] && append-fflags -i8 - fi - - [[ ${_bitness} == 64 ]] && \ - append-cflags "-DINTEGER='long long int'" - - # Set up location for the build directory - # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION - cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ - -i "${S}"/cns_solve_env || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ - -i "${T}"/cns_solve_env_sh || die - - einfo "Fixing shebangs..." - find "${S}" -type f \ - -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die -} - -src_compile() { - local GLOBALS - local MALIGN - if [[ $(tc-getFC) =~ g77 ]]; then - GLOBALS="-fno-globals" - MALIGN='\$(CNS_MALIGN_I86)' - fi - - # Set up the compiler to use - ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die - - # make install really means build, since it's expected to be used in-place - # -j1 doesn't mean we do no respect MAKEOPTS! - emake -j1 \ - CC="$(tc-getCC)" \ - F77=$(tc-getFC) \ - LD=$(tc-getFC) \ - CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ - LDFLAGS="${LDFLAGS}" \ - F77OPT="${FCFLAGS} ${MALIGN}" \ - F77STD="${GLOBALS}" \ - OMPLIB="${OMPLIB}" \ - compiler="${COMP}" \ - install -} - -src_test() { - # We need to force on g77 manually, because we can't get aliases working - # when we source in a -c - einfo "Running tests ..." - csh -c \ - "export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \ - || die "tests failed" - einfo "Displaying test results ..." - cat "${S}"/*_g77/test/*.diff-test -} - -src_install() { - # Install to locations resembling FHS - sed \ - -e "s:${S}:usr:g" \ - -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \ - -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \ - -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ - -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ - -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ - -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ - -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ - -e "/^g77on/d" \ - -i "${S}"/cns_solve_env || die - # I don't entirely understand why the sh version requires a leading / - # for CNS_SOLVE and CNS_ROOT, but it does - sed \ - -e "s:${S}:/usr:g" \ - -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \ - -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ - -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ - -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ - -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ - -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ - -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ - -e "/^g77on/d" \ - -e "/^g77off/d" \ - -i "${T}"/cns_solve_env_sh || die - - # Get rid of setup stuff we don't need in the installed script - sed \ - -e "83,$ d" \ - -e "37,46 d" \ - -i "${S}"/cns_solve_env || die - sed \ - -e "84,$ d" \ - -e "39,50 d" \ - -i "${T}"/cns_solve_env_sh || die - - newbin "${S}"/*linux*/bin/cns_solve* cns_solve - - # Can be run by either cns_solve or cns - dosym cns_solve /usr/bin/cns - - # Don't want to install this - rm -f "${S}"/*linux*/utils/Makefile || die - - dobin "${S}"/*linux*/utils/* - - sed \ - -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ - -i "${S}"/bin/cns_web || die - - dobin "${S}"/bin/cns_{edit,header,transfer,web} - - insinto /usr/share/cns - doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib - doins "${S}"/bin/cns_info - - insinto /etc/profile.d - newins "${S}"/cns_solve_env cns_solve_env.csh - newins "${T}"/cns_solve_env_sh cns_solve_env.sh - - dohtml \ - -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ - -f all_cns_info_template,omac,def \ - -r doc/html/* - # Conflits with app-text/dos2unix - rm -f "${D}"/usr/bin/dos2unix || die -} - -pkg_postinst() { - if use openmp; then - elog "Set OMP_NUM_THREADS to the number of threads you want." - elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" - elog "variable if using gcc (16384 should be good)." - fi -} diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild deleted file mode 100644 index 327d14b2488e..000000000000 --- a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild +++ /dev/null @@ -1,215 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic - -MY_PN="${PN}_solve" -MY_PV="$(delete_version_separator 2)" -MY_P="${MY_PN}_${MY_PV}" - -DESCRIPTION="Crystallography and NMR System" -HOMEPAGE="http://cns.csb.yale.edu/" -SRC_URI=" - ${MY_P/p7}_all.tar.gz - aria? ( aria2.3.1.tar.gz )" - -SLOT="0" -LICENSE="cns" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="aria openmp" - -RDEPEND="app-shells/tcsh" -DEPEND="${RDEPEND}" - -FORTRAN_NEED_OPENMP=1 - -S="${WORKDIR}/${MY_P/p7}" - -RESTRICT="fetch" - -pkg_nofetch() { - elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" - use aria && elog "and http://aria.pasteur.fr/" - elog "and place these files:" - elog ${A} - elog "into your DISTDIR directory." -} - -get_fcomp() { - case $(tc-getFC) in - *gfortran* ) - FCOMP="gfortran" ;; - ifort ) - FCOMP="ifc" ;; - * ) - FCOMP=$(tc-getFC) ;; - esac -} - -pkg_setup() { - fortran-2_pkg_setup - get_fcomp -} - -get_bitness() { - echo > "${T}"/test.c - $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o - case $(file "${T}"/test.o) in - *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; - *32-bit*|*ppc*|*i386*) export _bitness="32";; - *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; - esac -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PV}-gentoo.patch \ - "${FILESDIR}"/${PV}-delete.patch - - get_bitness - - if use aria; then - pushd "${WORKDIR}"/aria* >& /dev/null - # Update the cns sources in aria for version 1.2.1 - epatch "${FILESDIR}"/1.2.1-aria2.3.patch - - # Update the code with aria specific things - cp -rf cns/src/* "${S}"/source/ || die - popd >& /dev/null - fi - - # the code uses Intel-compiler-specific directives - if [[ $(tc-getFC) =~ gfortran ]]; then - use openmp && \ - append-flags -fopenmp && append-ldflags -fopenmp - COMP="gfortran" - [[ ${_bitness} == 64 ]] && \ - append-fflags -fdefault-integer-8 - elif [[ $(tc-getFC) == if* ]]; then - use openmp && \ - append-flags -openmp && append-ldflags -openmp - COMP="ifort" - [[ ${_bitness} == 64 ]] && append-fflags -i8 - fi - - [[ ${_bitness} == 64 ]] && \ - append-cflags "-DINTEGER='long long int'" - - # Set up location for the build directory - # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION - cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ - -i "${S}"/cns_solve_env || die - sed \ - -e "s:_CNSsolve_location_:${S}:g" \ - -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ - -e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \ - -e "s:^limit:^ulimit:g" \ - -i "${T}"/cns_solve_env_sh || die - - ebegin "Fixing shebangs..." - find "${S}" -type f \ - -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die - find . -name "Makefile*" \ - -exec \ - sed \ - -e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \ - -e "s:/bin/ls:ls:g" \ - -e "s:/bin/rm:rm:g" \ - -i '{}' + || die - eend -} - -src_compile() { - local GLOBALS - local MALIGN - - # Set up the compiler to use - ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die - - # make install really means build, since it's expected to be used in-place - # -j1 doesn't mean we do no respect MAKEOPTS! - emake -j1 \ - CC="$(tc-getCC)" \ - CXX="$(tc-getCXX)" \ - F77=$(tc-getFC) \ - LD=$(tc-getFC) \ - CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ - CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ - LDFLAGS="${LDFLAGS}" \ - F77OPT="${FCFLAGS} ${MALIGN}" \ - F77STD="${GLOBALS}" \ - OMPLIB="${OMPLIB}" \ - compiler="${COMP}" \ - install -} - -src_test() { - # We need to force on g77 manually, because we can't get aliases working - # when we source in a -c - einfo "Running tests ..." - sh -c \ - "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ - || die "tests failed" - einfo "Displaying test results ..." - cat "${S}"/*_g77/test/*.diff-test -} - -src_install() { - cat >> "${T}"/66cns <<- EOF - CNS_SOLVE="${EPREFIX}/usr" - CNS_ROOT="${EPREFIX}/usr" - CNS_DATA="${EPREFIX}/usr/share/cns" - CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3" - CNS_LIB="${EPREFIX}/usr/share/cns/libraries" - CNS_MODULE="${EPREFIX}/usr/share/cns/modules" - CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar" - CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb" - CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal" - CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr" - CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray" - CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal" - CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr" - CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib" - EOF - - doenvd "${T}"/66cns || die - - # Don't want to install this - rm -f "${S}"/*linux*/utils/Makefile || die - - sed \ - -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ - -i "${S}"/bin/cns_web || die - - newbin "${S}"/*linux*/bin/cns_solve* cns_solve - - # Can be run by either cns_solve or cns - dosym cns_solve /usr/bin/cns - - dobin \ - "${S}"/*linux*/utils/* \ - "${S}"/bin/cns_{edit,header,import_cif,transfer,web} - - insinto /usr/share/cns - doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info - - dohtml \ - -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ - -f all_cns_info_template,omac,def \ - -r doc/html/* - # Conflits with app-text/dos2unix - rm -f "${D}"/usr/bin/dos2unix || die -} - -pkg_postinst() { - if use openmp; then - elog "Set OMP_NUM_THREADS to the number of threads you want." - elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" - elog "variable if using gcc (16384 should be good)." - fi -} diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch deleted file mode 100644 index 42b9b0572231..000000000000 --- a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- source/xfft.f.orig 2008-08-03 00:36:52.000000000 -0700 -+++ source/xfft.f 2008-08-03 00:37:06.000000000 -0700 -@@ -514,7 +514,7 @@ - LOGICAL QHERM - DOUBLE PRECISION XRCELL(9), MAPR - C local --!$ integer omp_get_max_threads, kmp_get_stacksize -+!$ integer omp_get_max_threads - LOGICAL DONE - DOUBLE PRECISION ZERO - PARAMETER (ZERO=0.0D0) -@@ -537,7 +537,7 @@ - NBPP=1 - ! The following command is only relevant for the ifort compiler (if -openmp option is used). - ! If your compiler is not ifort, and gives an error, just comment the next line out: --!$ if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) -+! if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) - ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, - ! and 2**22 bytes (4Mb) for 64bit. - ! This may be low for big structures, which leads to segmentation faults! diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch deleted file mode 100644 index 8c6939d8eb92..000000000000 --- a/sci-chemistry/cns/files/1.2.1-aria2.3.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/cns/src/cns.f b/cns/src/cns.f -index a3c2cbe..51a34f8 100644 ---- a/cns/src/cns.f -+++ b/cns/src/cns.f -@@ -470,6 +470,7 @@ C local - INTEGER HNLEN, TMP, PTRSZ, STLEN - CHARACTER*(1) CNSPTMP - CHARACTER*(4) ST -+!$ integer omp_get_max_threads - C - C write header - WRITE(6,'(10X,A)') -@@ -526,6 +527,9 @@ C - WRITE(6,'(10X,7A)') - & ' Running on machine: ',HOSTNM(1:HNLEN), - & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)' -+!$ write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(), -+!$ & ' threads' -+!$C (to change use setenv OMP_NUM_THREADS x) - C - CALL GETNAM(USERNM,12,TMP) - WRITE(6,'(10X,2A)') diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch deleted file mode 100644 index 2b47bfcc7d86..000000000000 --- a/sci-chemistry/cns/files/1.2.1-gentoo.patch +++ /dev/null @@ -1,63 +0,0 @@ ---- cns_solve_1.21/instlib/source/Makefile.proto 2000-09-07 20:35:33.000000000 +0200 -+++ cns_solve_1.21/instlib/source/Makefile.proto.new 2009-07-14 09:18:37.000000000 +0200 -@@ -11,6 +11,8 @@ - - SHELL=/bin/sh - -+cns_string=`date "+%y%m%d%H%M"` -+ - # commands - RM = /bin/rm - -@@ -25,26 +27,20 @@ - - # rule for the fortran routines - $(OBJS): -- @ echo "compiling: $(@:.o=.f)"; \ -- $(F77) -c $(F77FLAGS) $(@:.o=.f) -+ $(F77) -c $(F77FLAGS) $(@:.o=.f) - - # rule for the dynamic memory allocation C routines - dmemory.o: dmemory.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the machine specific C routines - machine_c.o: machine_c.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the executable itself - ../bin/cns_solve: $(DEPENDS) -- @ echo ; echo "linking: cns_solve"; echo -- @ cns_string=`date "+%y%m%d%H%M"`; \ -- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -- $(LDFLAGS) \ -- $(CNS_FFTDIR) $(CNS_FFTLIB); \ -+ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -+ $(CNS_FFTDIR) $(CNS_FFTLIB); \ - if [ -x cns_solve-$$cns_string.exe ]; \ - then echo "created executable file cns_solve-$$cns_string.exe"; \ - echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ ---- cns_solve_1.21/instlib/utils/Makefile 2004-08-30 00:40:35.000000000 +0200 -+++ cns_solve_1.21/instlib/utils/Makefile.new 2009-07-14 09:50:27.000000000 +0200 -@@ -22,14 +22,14 @@ - make clean - - .f: -- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) -+ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) - - .c: -- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) -+ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) - - .l: - lex $(@).l -- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) -+ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) - - relink: - @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch deleted file mode 100644 index ba44bebd1b68..000000000000 --- a/sci-chemistry/cns/files/1.2.1-ifort.patch +++ /dev/null @@ -1,126 +0,0 @@ -diff --git a/source/angledb.f b/source/angledb.f -index 28ad657..eaa847d 100644 ---- a/source/angledb.f -+++ b/source/angledb.f -@@ -1416,10 +1416,10 @@ C include files - C local variables - INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS - INTEGER THETYPE, CURPSIS, CURPHIS -- INTEGER CLASSINDEX -+ INTEGER CLASINDEX - DOUBLE PRECISION K1, CUTOFF - CHARACTER*4 THENAME -- CHARACTER*20 CLASSNAME -+ CHARACTER*20 CLASNAME - C begin - C - IF (ANGLEDBFLAG) THEN -@@ -1450,10 +1450,10 @@ C - ELSE IF (WD(1:4).EQ.'CLAS') THEN - OLDCLASS = CURANGLEDBCLASS - CALL NEXTWD('class name =') -- CLASSNAME = WD(1:20) -+ CLASNAME = WD(1:20) - ANGLEDBMODE = NEW - DO COUNT = 1, NANGLEDBCLASSES -- IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN -+ IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN - ANGLEDBMODE = UPDATE - CURANGLEDBCLASS = COUNT - END IF -@@ -1472,7 +1472,7 @@ C - END IF - NANGLEDBCLASSES = NANGLEDBCLASSES + 1 - CURANGLEDBCLASS = NANGLEDBCLASSES -- ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME -+ ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME - ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS - END IF - C -@@ -1733,16 +1733,16 @@ C - & HEAP(ANGLEDBTPTR)) - ELSE IF (WD(1:4).EQ.'CLAS') THEN - CALL NEXTWD('Class name>') -- CLASSNAME = WD(1:20) -- CLASSINDEX = 0 -+ CLASNAME = WD(1:20) -+ CLASINDEX = 0 - DO COUNT = 1, NANGLEDBCLASSES - IF (ANGDBCLASSNAMES(COUNT).EQ. -- & CLASSNAME) THEN -+ & CLASNAME) THEN - PRINTTHISCLASS(COUNT) = .TRUE. -- CLASSINDEX = COUNT -+ CLASINDEX = COUNT - END IF - END DO -- IF (CLASSINDEX.EQ.0) THEN -+ IF (CLASINDEX.EQ.0) THEN - CALL DSPERR('ANGLEDB', - & 'unknown class. Using first.') - PRINTTHISCLASS(1) = .TRUE. -diff --git a/source/rama.f b/source/rama.f -index c5d14f2..3063e7b 100644 ---- a/source/rama.f -+++ b/source/rama.f -@@ -1468,11 +1468,11 @@ C include files - C local variables - INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS, - & THETYPE, CURPSIS, CURPHIS, -- & CURCHIS, CURTHTS, CLASSINDEX -+ & CURCHIS, CURTHTS, CLASINDEX - INTEGER CLEN - DOUBLE PRECISION K1, CUTOFF - CHARACTER*4 THENAME -- CHARACTER*50 CLASSNAME -+ CHARACTER*50 CLASNAME - C begin - C - C this is used by READRAMA2 to hold the selection -@@ -1503,10 +1503,10 @@ C - ELSE IF (WD(1:4).EQ.'CLAS') THEN - OLDCLASS = CURRAMACLASS - CALL NEXTWD('class name =') -- CLASSNAME = WD(1:50) -+ CLASNAME = WD(1:50) - RAMAMODE = NEW - DO COUNT = 1, NRAMACLASSES -- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN -+ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN - RAMAMODE = UPDATE - CURRAMACLASS = COUNT - END IF -@@ -1525,7 +1525,7 @@ C - END IF - NRAMACLASSES = NRAMACLASSES + 1 - CURRAMACLASS = NRAMACLASSES -- RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME -+ RAMACLASSNAMES(CURRAMACLASS) = CLASNAME - END IF - C - C set force constant for current class, -@@ -1954,18 +1954,18 @@ C - & HEAP(RAMAATOMPTR), 0) - ELSE IF (WD(1:4).EQ.'CLAS') THEN - CALL NEXTWD('Class name>') -- CLASSINDEX = 0 -+ CLASINDEX = 0 - DO COUNT = 1, NRAMACLASSES -- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) -- & CLASSINDEX = COUNT -+ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) -+ & CLASINDEX = COUNT - END DO -- IF (CLASSINDEX.EQ.0) THEN -+ IF (CLASINDEX.EQ.0) THEN - CALL DSPERR('RAMA', - & 'unknown class. Using first.') -- CLASSINDEX = 1 -+ CLASINDEX = 1 - END IF - CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR), -- & HEAP(RAMAATOMPTR), CLASSINDEX) -+ & HEAP(RAMAATOMPTR), CLASINDEX) - ELSE - CALL DSPERR('RAMA', - & 'Expected ALL or CLASs.') diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch deleted file mode 100644 index dfaa40021d66..000000000000 --- a/sci-chemistry/cns/files/1.2.1-parallel.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto -index 0d0dd3e..ae9e422 100644 ---- a/instlib/source/Makefile.proto -+++ b/instlib/source/Makefile.proto -@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o - - # the default is to make the cns executable - cns_solve: -- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k exepurge -+ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make exepurge - - # rule for the fortran routines - $(OBJS): diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch deleted file mode 100644 index cbddf4289158..000000000000 --- a/sci-chemistry/cns/files/1.3_p7-delete.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp -index b64467a..5f727db 100644 ---- a/utils/cluster_struc.cpp -+++ b/utils/cluster_struc.cpp -@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) { - for (int i = 0; i < nrstruc; i++) { - delete[] neighbor[i]; - } -- delete[] neighbor, neighborcount; -+ delete[] neighbor, delete[] neighborcount; - return 5; - } - if (rmsd < cutoff) { diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch deleted file mode 100644 index 7942c55abfb9..000000000000 --- a/sci-chemistry/cns/files/1.3_p7-gentoo.patch +++ /dev/null @@ -1,80 +0,0 @@ -diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto -index 0d0dd3e..dd4b680 100644 ---- a/instlib/source/Makefile.proto -+++ b/instlib/source/Makefile.proto -@@ -11,6 +11,8 @@ - - SHELL=/bin/sh - -+cns_string=`date "+%y%m%d%H%M"` -+ - # commands - RM = /bin/rm - -@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o - - # the default is to make the cns executable - cns_solve: -- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -- @ make -k exepurge -+ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" -+ @ make exepurge - - # rule for the fortran routines - $(OBJS): -- @ echo "compiling: $(@:.o=.f)"; \ -- $(F77) -c $(F77FLAGS) $(@:.o=.f) -+ $(F77) -c $(F77FLAGS) $(@:.o=.f) - - # rule for the dynamic memory allocation C routines - dmemory.o: dmemory.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the machine specific C routines - machine_c.o: machine_c.c -- @ echo ; echo "compiling: $?" -- @ $(CC) -c $(CCFLAGS) $? -+ $(CC) -c $(CCFLAGS) $? - - # rule for the executable itself - ../bin/cns_solve: $(DEPENDS) -- @ echo ; echo "linking: cns_solve"; echo -- @ cns_string=`date "+%y%m%d%H%M"`; \ -- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -- $(LDFLAGS) \ -- $(CNS_FFTDIR) $(CNS_FFTLIB); \ -+ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ -+ $(CNS_FFTDIR) $(CNS_FFTLIB); \ - if [ -x cns_solve-$$cns_string.exe ]; \ - then echo "created executable file cns_solve-$$cns_string.exe"; \ - echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ -diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile -index 98de84f..4f32b34 100644 ---- a/instlib/utils/Makefile -+++ b/instlib/utils/Makefile -@@ -22,17 +22,17 @@ utils: - make clean - - .f: -- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) -+ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) - - .c: -- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) -+ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) - - .cpp: -- $(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK) -+ $(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK) - - .l: - lex $(@).l -- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) -+ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) - - relink: - @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh deleted file mode 100644 index 34e1a2b635cf..000000000000 --- a/sci-chemistry/cns/files/cns_solve_env_sh +++ /dev/null @@ -1,221 +0,0 @@ -#!/bin/sh -# -# This file sets up the appropriate environmental variables and paths -# for CNSsolve. In the case of the same machines with different versions -# of the OS, backward compatibility is assumed - ie. a later version will -# be setup for a previous version of the OS if nothing else is available. -# -# written by: Paul Adams -# -# copyright Yale University -# -# ========================================================================== -# -# >>>>>> Important: define the location of the CNSsolve directory <<<<<< -# -# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY - - CNS_SOLVE=_CNSsolve_location_ - -# -# ========================================================================== -# -# full expansion of the CNS_SOLVE variable prior to use. -# -export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE -# -# ========================================================================== -# -# set the number of threads for SGI multiprocessors -# if this causes a problem on other systems it can be commented out -# -export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1 -# -# ========================================================================== -# -# get the machine architecture -# -if [ -d $CNS_SOLVE ]; then - if [ ! "$CNS_ARCH" ]; then - export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` - fi -else - export CNS_ARCH; CNS_ARCH='unknown' -fi -# -# system variables (this is needed for openmp) -# -ulimit -s unlimited -# ========================================================================== -# -# general environmental variables -# -export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries -export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules -export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar -export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb -export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal -export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr -export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray -export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal -export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr -export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib -# -# general user aliases -# -cns_web () { $CNS_SOLVE/bin/cns_web; } -cns_header () { $CNS_SOLVE/bin/cns_header; } -cns_info () { cat $CNS_SOLVE/bin/cns_info; } -cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } -if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then - cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } -else - cns_edit () { $CNS_SOLVE/bin/cns_edit; } -fi -run_tutorial () { "csh -f tutorial.csh"; } -# -# g77 compilation and use -# -g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } -g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } -# -# developer aliases -# -run_tests () { $CNS_SOLVE/bin/run_tests; } -run_diffs () { $CNS_SOLVE/bin/run_diffs; } -maketar () { $CNS_SOLVE/bin/maketar; } -create_patch () { $CNS_SOLVE/bin/create_patch; } -# -# -# ========================================================================== -# -# to do expansions - unset noglob just in case user has it otherwise -# -set +f -# -# try to set up appropriate path -# -# first strip off any trailing information (eg. _g77) -# -CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` -# -cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` -cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` -cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` -cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` -cns_minor=`echo $cns_major | sed -e 's/\./ /g'` -# -# if we are looking for a specific type of setup then limit search -# -cns_dirs="" -if [ ! "$CNS_G77" ]; then - if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -else - CNS_ARCH="${CNS_ARCH}_g77" - if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -fi -# -# first look for an exact match (with os version) -# -# -cns_found=0 -if [ -n "$cns_dirs" ]; then - for cns_dir in $cns_dirs ; do - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done -# -# -# now look for an exact match (without os version) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done - fi -# -# now look for a backwards compatible match (with os version major/minor) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then - osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` - if [ $osv_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -# -# now look for a wildcard match on cpu -# - if [ $cns_found -eq 0 ]; then - cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` - cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` - cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then - cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` - if [ $cpu_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -fi -# -# if found set environment -# -if [ $cns_found -eq 1 ]; then - # - # set installation and source directory - # - export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv - export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source - # - # path for CNSsolve utility programs - # - if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` - fi - # - # path for CNSsolve executable if installed - # - if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` - fi -fi -# -unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor -unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same -unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test -# diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 deleted file mode 100644 index 12368f87b596..000000000000 --- a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 +++ /dev/null @@ -1,229 +0,0 @@ -#!/bin/sh -# -# This file sets up the appropriate environmental variables and paths -# for CNSsolve. In the case of the same machines with different versions -# of the OS, backward compatibility is assumed - ie. a later version will -# be setup for a previous version of the OS if nothing else is available. -# -# written by: Paul Adams -# -# copyright Yale University -# -# ========================================================================== -# -# >>>>>> Important: define the location of the CNSsolve directory <<<<<< -# -# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY - - CNS_SOLVE=_CNSsolve_location_ - -# -# ========================================================================== -# -# full expansion of the CNS_SOLVE variable prior to use. -# -export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE -# -# ========================================================================== -# -# get the machine architecture -# -if [ -d $CNS_SOLVE ]; then - if [ ! "$CNS_ARCH" ]; then - export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` - fi -else - export CNS_ARCH; CNS_ARCH='unknown' -fi -# -# ========================================================================== -# -# system variables for OpenMP -# -# The default stack sizes are usually insufficient, especially when -# CNS is compiled using OpenMP. If the stack sizes are too -# small segfaults may occur. Recommended setting for "stacksize": -limit stacksize unlimited -# -# KMP_STACKSIZE is specific for Intel ifort, icc: -##setenv KMP_STACKSIZE 256m -# -# OMP_STACKSIZE is used by all compilers: -setenv OMP_STACKSIZE 256m -# -# Uncomment the following line and change as appropriate to set the number -# of processors (threads) to use. -###setenv OMP_NUM_THREADS 4 -# -# ========================================================================== -# -# general environmental variables -# -export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries -export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules -export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar -export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb -export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal -export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr -export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray -export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal -export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr -export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib -# -# general user aliases -# -cns_web () { $CNS_SOLVE/bin/cns_web; } -cns_header () { $CNS_SOLVE/bin/cns_header; } -cns_info () { cat $CNS_SOLVE/bin/cns_info; } -cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } -if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then - cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } -else - cns_edit () { $CNS_SOLVE/bin/cns_edit; } -fi -# -# g77 compilation and use -# -g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } -g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } -# -# developer aliases -# -run_tests () { $CNS_SOLVE/bin/run_tests; } -run_diffs () { $CNS_SOLVE/bin/run_diffs; } -maketar () { $CNS_SOLVE/bin/maketar; } -create_patch () { $CNS_SOLVE/bin/create_patch; } -# -# -# ========================================================================== -# -# to do expansions - unset noglob just in case user has it otherwise -# -set +f -# -# try to set up appropriate path -# -# first strip off any trailing information (eg. _g77) -# -CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` -# -cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` -cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` -cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` -cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` -cns_minor=`echo $cns_major | sed -e 's/\./ /g'` -# -# if we are looking for a specific type of setup then limit search -# -cns_dirs="" -if [ ! "$CNS_G77" ]; then - if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -else - CNS_ARCH="${CNS_ARCH}_g77" - if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then - cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" - fi -fi -# -# first look for an exact match (with os version) -# -# -cns_found=0 -if [ -n "$cns_dirs" ]; then - for cns_dir in $cns_dirs ; do - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done -# -# -# now look for an exact match (without os version) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ - $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - done - fi -# -# now look for a backwards compatible match (with os version major/minor) -# - if [ $cns_found -eq 0 ]; then - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then - osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` - if [ $osv_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -# -# now look for a wildcard match on cpu -# - if [ $cns_found -eq 0 ]; then - cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` - cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` - for cns_dir in $cns_dirs ; do - if [ $cns_found -eq 0 ]; then - cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` - cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` - if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then - if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ - $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then - cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` - if [ $cpu_test -eq 1 ]; then - cns_archenv=$cns_dir - cns_found=1 - fi - fi - fi - fi - done - fi -fi -# -# if found set environment -# -if [ $cns_found -eq 1 ]; then - # - # set installation and source directory - # - export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv - export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source - # - # path for CNSsolve utility programs - # - if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` - fi - # - # path for CNSsolve executable if installed - # - if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then - export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` - fi -fi -# -unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor -unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same -unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test -# diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml deleted file mode 100644 index 67326b6bd798..000000000000 --- a/sci-chemistry/cns/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <use> - <flag name="aria"> Support patch for sci-chemistry/aria</flag> - </use> - <longdescription> -Crystallography and NMR System (CNS) is the result of an international -collaborative effort among several research groups. The program has -been designed to provide a flexible multi-level hierachical approach for the -most commonly used algorithms in macromolecular structure determination. -Highlights include heavy atom searching, experimental phasing (including -MAD and MIR), density modification, crystallographic refinement with maximum -likelihood targets, and NMR structure calculation using NOEs, J-coupling, -chemical shift, and dipolar coupling data. -</longdescription> -</pkgmetadata> |