From af2d23a6e79abd8092230d1045f9f689a776589b Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Thu, 28 Jul 2011 16:02:48 +0400 Subject: [sci-chemistry/ambertools] Updates for ambertools and gcc-4.6 (Portage version: 2.2.0_alpha47/git/Linux x86_64, signed Manifest commit with key F82F92E6) --- sci-chemistry/ambertools/Manifest | 20 +++- sci-chemistry/ambertools/ambertools-1.5-r1.ebuild | 140 ++++++++++++++++++++++ 2 files changed, 156 insertions(+), 4 deletions(-) create mode 100644 sci-chemistry/ambertools/ambertools-1.5-r1.ebuild (limited to 'sci-chemistry/ambertools') diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest index 98d79e2e3..0636d23e2 100644 --- a/sci-chemistry/ambertools/Manifest +++ b/sci-chemistry/ambertools/Manifest @@ -1,20 +1,32 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 +Hash: SHA256 AUX ambertools-1.4-gentoo.patch 9926 RMD160 d84b121e1fa940cbf949855de3a5f0bee7566330 SHA1 08ea41b969bed5320230420d047e71a28333f76c SHA256 8f520c01146a704173ca31c68dc9440e2938263416f6d0c95de22d138426e01f AUX ambertools-1.5-gentoo.patch 14083 RMD160 762c52626c4eda51839caf74c001bb660052706a SHA1 ab0afa1f5b73569539515dba4cf6638a594c7d6e SHA256 82a83f660701c192272e79f5bab17a8a8be945d78fdab454ade3918281749922 DIST AmberTools-1.4.tar.bz2 67331137 RMD160 b499e18b583a0b454dd3a554986c19c111822e6a SHA1 ef0f9a44c8767ed35f942fd41afc636b67da0389 SHA256 af61da2f3643b4ec7f41620242b734a3cb4a79c5d422100fbd1fd1c402fecfc1 DIST AmberTools-1.5.tar.bz2 121062582 RMD160 4a086b42c378f0904f7bf0b16adb042f1677be55 SHA1 92e47e7337fb4901a5a145d808c5ffd42c82d08d SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c DIST ambertools-1.4-bugfix_1-18.patch.xz 48136 RMD160 83fe98ef2f4620cd4c85fc72147f830ddfa47b51 SHA1 7a5a2cba9172d017d83aed16ece06d6fed6a5196 SHA256 7ea936442ce1b29943e867adaeb69932d297ae50e0a63b0e03cfb18953e9f7c2 +DIST ambertools-1.5-bugfix_1-10.patch.xz 38396 RMD160 680e64bb7071ea126650c79cd41fc9b8272207bd SHA1 1aec1063902cd3681550f04ba106a14b6b2aaa37 SHA256 469a45b079a3b67a2b58bc6d4dcc46a115305869ddf4ab5890f293e1c5ec05f7 DIST ambertools-1.5-bugfix_1-3.patch.xz 27268 RMD160 18a74e2e84e81d39417f656ef93e8ee4d4d4583d SHA1 bc52c0776d151a8db005bb7bfb40bf9e963bdeba SHA256 edec6ccc275ee0a70b2ecc9316c031249c4f32d89b1aa145cee32c862516049a EBUILD ambertools-1.4.ebuild 3201 RMD160 b2f4331166bafc5093f04c4e7ad9bf2eee9ee0e5 SHA1 4033d6225f7e86d42292eed5ddecd7edeb6742ec SHA256 e3a77f1a006832c46117a5c6a6a641685965f8dfe0c949c0ec1e2f7e57f73835 +EBUILD ambertools-1.5-r1.ebuild 3337 RMD160 a5826024f12a9a070c4f1cdd87878d09f3ba62de SHA1 97e45fbbaf16b126d240d95c3fc3896e372f5086 SHA256 d07ed914b461ebb2a0443b6fb0b334f2912e7e3a0f77ee9a44fce0b75f3580ea EBUILD ambertools-1.5.ebuild 3336 RMD160 d97fc7eade8bcf0d12596d42a512560671751d18 SHA1 0427a45349e95be91e274d0e12eb2eb484da6dd3 SHA256 8f8f33770cb12253fef10e9b651a567de36a2863d674b82ca3b1959ab8684353 MISC ChangeLog 979 RMD160 02da25807e2c08495e5e6ed5803c8db37b6f0630 SHA1 086394d21356fb100929d5f86e86a098d34abe43 SHA256 c3cf8fabe0c249e1b500319df8296405392fa976fb599d941544af342d292aec MISC metadata.xml 263 RMD160 9484584cc295931e963dc785e211261f68e48c82 SHA1 a2c5af57c8eb879a4249fc0240432a4fc5b91ca5 SHA256 0e94df6d8502bc41ccd18ec4d570490e245c08595e837fd116a255458939e69b -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) -iEYEARECAAYFAk4E9DkACgkQgAnW8HDreRa8NwCg0fxLgoMsWuqoreVAAV0tzOgb -Bp4An3RO97c8j9rzfFLDjx6ix2ySY7kE -=zAXR +iQIcBAEBCAAGBQJOMU/oAAoJEOf+E+/4L5Lmz+MQAKNWWfnkOntA2yFblWcxSdt/ +QvvzY18t67Y3ZhKunWd1iQcj1FEWYdOjLEkRKbUkI9aK4RqPoHTz5TgYMp1aI7Kx +GZuUuh5vP5O+Vsl5AgqOnx9IU9A09JsmxhvAoFOA++2XIUdqTwjuCBHOvxbcRSDK +d+4hnMU919oCO6xgsePAxhxoMIrW1RCz52MBfpzpshTbYGfJiIgbqcWKH9FgQ3Fn +QZg8TScUcpT0nvqnqVjp/HycKbspagALNrw6ePutJL67+p8uYzyUvJ9f+VhwZOod +qPBZ/alGIebQpeZqpk17snWxJVvhDBWNANFg3S39T7UGst+I6RR7OjFFsJ6ZC5VY +Uy65pDK1If7eYnoWBUEL+hWrg2bfv/Xn+eEd+W9pn/FDTLpw4CznZZX8TNLz+ipP +Q1EGidSrkZrM0nJriuH75hilCrJeLZFlDGsDNzSaxBNqHRAo1PfgtkG0HlAmJEFN 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+RDEPEND=" + virtual/cblas + virtual/lapack + sci-libs/clapack + sci-libs/arpack + sci-libs/cifparse-obj + sci-chemistry/mopac7 + sci-libs/netcdf + sci-libs/fftw:2.1 + sci-chemistry/reduce + virtual/fortran" +DEPEND="${RDEPEND} + dev-util/byacc + dev-libs/libf2c + sys-devel/ucpp" +S="${WORKDIR}/amber11" + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${A}" + einfo "Place it in ${DISTDIR}" +} + +pkg_setup() { + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi + AMBERHOME="${S}" +} + +src_prepare() { + epatch \ + "${WORKDIR}/${P}-bugfix_1-3.patch" \ + "${FILESDIR}/${P}-gentoo.patch" + cd AmberTools/src + rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die +} + +src_configure() { + cd AmberTools/src + sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ + -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ + -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ + -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ + -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \ + -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \ + -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \ + -e "s:fc=g77:fc=$(tc-getFC):g" \ + -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ + -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ + -e "s:-O3::g" \ + -i configure || die + sed -e "s:arsecond_:arscnd_:g" \ + -i sff/time.c \ + -i sff/sff.h \ + -i sff/sff.c || die + sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ + -i nss/Makefile || die + + local myconf + + use X || myconf="${myconf} -noX11" + + for x in mpi openmp; do + use ${x} && myconf="${myconf} -${x}" + done + + ./configure \ + ${myconf} \ + -nobintraj \ + -nomdgx \ + -nopython \ + -nomtkpp \ + gnu +# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') +} + +src_compile() { + cd AmberTools/src + emake || die +} + +src_install() { + rm -r bin/chemistry bin/MMPBSA_mods + rm bin/ante-MMPBSA.py bin/extractFrcmod.py + for x in bin/* + do dobin ${x} || die + done + rm "${ED}/usr/bin/yacc" + dobin AmberTools/src/antechamber/mopac.sh + sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ + -i "${ED}/usr/bin/mopac.sh" || die + # Make symlinks untill binpath for amber will be fixed + dodir /usr/share/${PN}/bin + cd "${ED}/usr/bin" + for x in * + do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} + done + cd "${S}" +# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ +# -i "${ED}/usr/bin/xleap" \ +# -i "${ED}/usr/bin/tleap" || die + dodoc doc/AmberTools.pdf doc/leap_pg.pdf + dolib.a lib/* + insinto /usr/include/${PN} + doins include/* + insinto /usr/share/${PN} + doins -r dat + cd AmberTools + doins -r benchmarks + doins -r examples + doins -r test + cat >> "${T}"/99ambertools <<- EOF + AMBERHOME="${EPREFIX}/usr/share/ambertools" + EOF + doenvd "${T}"/99ambertools +} 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