From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QmQKn-0001TF-9g for garchives@archives.gentoo.org; Thu, 28 Jul 2011 13:09:10 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B389121C15B; Thu, 28 Jul 2011 13:08:57 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id E41C721C15B for ; Thu, 28 Jul 2011 13:08:56 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 538D01B401A for ; Thu, 28 Jul 2011 13:08:56 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id C70718003D for ; Thu, 28 Jul 2011 13:08:55 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/ambertools/ChangeLog sci-chemistry/ambertools/ambertools-1.4.ebuild sci-chemistry/ambertools/ambertools-1.5-r1.ebuild sci-chemistry/ambertools/ambertools-1.5.ebuild sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch sci-chemistry/ambertools/metadata.xml X-VCS-Directories: sci-chemistry/ambertools/files/ sci-chemistry/ambertools/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: bbe17657b55b52de681189473db11225a8f82f2f Date: Thu, 28 Jul 2011 13:08:55 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 17c86db5e4c17c10cc9fb04a4cba4a84 commit: bbe17657b55b52de681189473db11225a8f82f2f Author: Alexey Shvetsov gentoo org> AuthorDate: Thu Jul 28 13:08:27 2011 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Thu Jul 28 13:08:27 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Dbbe17657 [sci-chemistry/ambertools] Moved to tree =3DD --- sci-chemistry/ambertools/ChangeLog | 29 -- sci-chemistry/ambertools/ambertools-1.4.ebuild | 133 ------- sci-chemistry/ambertools/ambertools-1.5-r1.ebuild | 140 ------- sci-chemistry/ambertools/ambertools-1.5.ebuild | 140 ------- .../ambertools/files/ambertools-1.4-gentoo.patch | 289 --------------= - .../ambertools/files/ambertools-1.5-gentoo.patch | 386 --------------= ------ sci-chemistry/ambertools/metadata.xml | 10 - 7 files changed, 0 insertions(+), 1127 deletions(-) diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertool= s/ChangeLog deleted file mode 100644 index d51fa1a..0000000 --- a/sci-chemistry/ambertools/ChangeLog +++ /dev/null @@ -1,29 +0,0 @@ -# ChangeLog for sci-chemistry/ambertools -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 24 Jun 2011; Justin Lecher ambertools-1.4.ebuild, - -files/ambertools-1.4-bugfix_1-18.patch, ambertools-1.5.ebuild, - -files/ambertools-1.5-bugfix_1-3.patch: - Cleaned ebuild - - 23 Jun 2011; Justin Lecher ambertools-1.4.ebuild, - ambertools-1.5.ebuild: - Streamlined fortran-2 eclass usage - - 21 Jun 2011; Justin Lecher ambertools-1.4.ebuild, - ambertools-1.5.ebuild: - Added fortran-2.eclass support - -*ambertools-1.5 (04 Jun 2011) - - 04 Jun 2011; Reinis Danne +ambertools-1.5.ebuild, - +files/ambertools-1.5-bugfix_1-3.patch, +files/ambertools-1.5-gentoo.p= atch: - Version bump. - - 15 Mar 2011; Justin Lecher ambertools-1.4.ebuild: - Remove fortran.eclass - - 14 Mar 2011; Justin Lecher ambertools-1.4.ebuild: - Remove fortran.eclass removal - diff --git a/sci-chemistry/ambertools/ambertools-1.4.ebuild b/sci-chemist= ry/ambertools/ambertools-1.4.ebuild deleted file mode 100644 index 5e75cdb..0000000 --- a/sci-chemistry/ambertools/ambertools-1.4.ebuild +++ /dev/null @@ -1,133 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION=3D"A suite for carrying out complete molecular mechanics inv= estigations" -HOMEPAGE=3D"http://ambermd.org/#AmberTools" -SRC_URI=3D" - AmberTools-${PV}.tar.bz2 - mirror://gentoo/${P}-bugfix_1-18.patch.xz" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"mpi openmp X" - -RESTRICT=3D"fetch" - -RDEPEND=3D" - virtual/cblas - virtual/lapack - sci-libs/arpack - sci-libs/cifparse-obj - sci-chemistry/mopac7 - sci-libs/netcdf - sci-chemistry/reduce - virtual/fortran" -DEPEND=3D"${RDEPEND} - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" -S=3D"${WORKDIR}/amber11" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get ${A}" - einfo "Place it in ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - if use openmp; then - tc-has-openmp || \ - die "Please select an openmp capable compiler like gcc[openmp]" - fi - AMBERHOME=3D"${S}" -} - -src_prepare() { - epatch \ - "${WORKDIR}/${P}-bugfix_1-18.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)/libdrfft= w.a:g" \ - -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw= .a:g" \ - -e "s:CFLAGS=3D:CFLAGS=3D${CFLAGS} -DBINTRAJ :g" \ - -e "s:FFLAGS=3D:FFLAGS=3D${FFLAGS} :g" \ - -e "s:LDFLAGS=3D$ldflags:LDFLAGS=3D${LDFLAGS}:g" \ - -e "s:fc=3Dg77:fc=3D$(tc-getFC):g" \ - -e "s:NETCDFLIB=3D\$netcdflib:NETCDFLIB=3D$(pkg-config netcdf --libs):= g" \ - -e "s:NETCDF=3D\$netcdf:NETCDF=3Dnetcdf.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=3D"${myconf} -noX11" - - for x in mpi openmp; do - use ${x} && myconf=3D"${myconf} -${x}" - done - - ./configure \ - ${myconf} \ - -nobintraj \ - gnu -# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') -} - -src_compile() { - cd AmberTools/src - emake || die -} - -src_install() { - 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=3D"${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chem= istry/ambertools/ambertools-1.5-r1.ebuild deleted file mode 100644 index da44cf5..0000000 --- a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild +++ /dev/null @@ -1,140 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION=3D"A suite for carrying out complete molecular mechanics inv= estigations" -HOMEPAGE=3D"http://ambermd.org/#AmberTools" -SRC_URI=3D" - AmberTools-${PV}.tar.bz2 - mirror://gentoo/${P}-bugfix_1-10.patch.xz" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"mpi openmp X" - -RESTRICT=3D"fetch" - -RDEPEND=3D" - 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=3D"${RDEPEND} - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" -S=3D"${WORKDIR}/amber11" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get ${A}" - einfo "Place it in ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - if use openmp; then - tc-has-openmp || \ - die "Please select an openmp capable compiler like gcc[openmp]" - fi - AMBERHOME=3D"${S}" -} - -src_prepare() { - epatch \ - "${WORKDIR}/${P}-bugfix_1-10.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)/libdrfft= w.a:g" \ - -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw= .a:g" \ - -e "s:CFLAGS=3D:CFLAGS=3D${CFLAGS} -DBINTRAJ :g" \ - -e "s:FFLAGS=3D:FFLAGS=3D${FFLAGS} :g" \ - -e "s:LDFLAGS=3D$ldflags:LDFLAGS=3D${LDFLAGS}:g" \ - -e "s:fc=3Dg77:fc=3D$(tc-getFC):g" \ - -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ - -e "s:NETCDF=3D\$netcdf:NETCDF=3Dnetcdf.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=3D"${myconf} -noX11" - - for x in mpi openmp; do - use ${x} && myconf=3D"${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=3D"${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/ambertools-1.5.ebuild b/sci-chemist= ry/ambertools/ambertools-1.5.ebuild deleted file mode 100644 index 9ac9755..0000000 --- a/sci-chemistry/ambertools/ambertools-1.5.ebuild +++ /dev/null @@ -1,140 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3D4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION=3D"A suite for carrying out complete molecular mechanics inv= estigations" -HOMEPAGE=3D"http://ambermd.org/#AmberTools" -SRC_URI=3D" - AmberTools-${PV}.tar.bz2 - mirror://gentoo/${P}-bugfix_1-3.patch.xz" - -LICENSE=3D"GPL-2" -SLOT=3D"0" -KEYWORDS=3D"~amd64 ~x86" -IUSE=3D"mpi openmp X" - -RESTRICT=3D"fetch" - -RDEPEND=3D" - 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=3D"${RDEPEND} - dev-util/byacc - dev-libs/libf2c - sys-devel/ucpp" -S=3D"${WORKDIR}/amber11" - -pkg_nofetch() { - einfo "Go to ${HOMEPAGE} and get ${A}" - einfo "Place it in ${DISTDIR}" -} - -pkg_setup() { - fortran-2_pkg_setup - if use openmp; then - tc-has-openmp || \ - die "Please select an openmp capable compiler like gcc[openmp]" - fi - AMBERHOME=3D"${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)/libdrfft= w.a:g" \ - -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw= .a:g" \ - -e "s:CFLAGS=3D:CFLAGS=3D${CFLAGS} -DBINTRAJ :g" \ - -e "s:FFLAGS=3D:FFLAGS=3D${FFLAGS} :g" \ - -e "s:LDFLAGS=3D$ldflags:LDFLAGS=3D${LDFLAGS}:g" \ - -e "s:fc=3Dg77:fc=3D$(tc-getFC):g" \ - -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ - -e "s:NETCDF=3D\$netcdf:NETCDF=3Dnetcdf.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=3D"${myconf} -noX11" - - for x in mpi openmp; do - use ${x} && myconf=3D"${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=3D"${EPREFIX}/usr/share/ambertools" - EOF - doenvd "${T}"/99ambertools -} diff --git a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch b= /sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch deleted file mode 100644 index c067928..0000000 --- a/sci-chemistry/ambertools/files/ambertools-1.4-gentoo.patch +++ /dev/null @@ -1,289 +0,0 @@ -diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/c= onfigure ---- amber11.orig/AmberTools/src/configure 2010-04-23 18:17:17.000000000 = +0400 -+++ amber11/AmberTools/src/configure 2011-03-07 03:39:14.000000000 +0300 -@@ -288,11 +288,11 @@ - mpi_flag=3D - lex=3Dflex - flibs_mkl=3D --lapack=3Dinstall --blas=3Dinstall -+lapack=3Dskip -+blas=3Dskip - f2c=3Dskip --ucpp=3Dinstall --cpp=3D"\$(BINDIR)/ucpp -l" -+ucpp=3Dskip -+cpp=3D"\$(EPREFIX)/usr/bin/ucpp -l" -=20 - #----------------------------------- - # skip building of sleap? -@@ -1241,24 +1241,24 @@ - #--------------------------------------------------------------------= ------ - # Configure fftw-3.2.2: - #--------------------------------------------------------------------= ------ -- if [ "$mdgx" =3D 'yes' ]; then -- mdgxflag=3D"--prefix=3D$AMBERHOME --disable-fortran"=20 -- echo -- echo "Configuring fftw-3.2.2; (may be time-consuming)" -- echo -- cd fftw-3.2.2 && \ -- env CC=3D"$cc" CFLAGS=3D"$cflags" ./configure $mdgxflag \ -- > ../fftw3_config.log 2>&1 -- ncerror=3D$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: fftw configure returned $ncerror" -- echo " fftw configure failed! Check the fftw3_config.log = file." -- exit 1 -- else -- echo " fftw-3.2.2 configure succeeded." -- fi -- cd .. -- fi -+ #if [ "$mdgx" =3D 'yes' ]; then -+ # mdgxflag=3D"--prefix=3D$AMBERHOME --disable-fortran"=20 -+ # echo -+ # echo "Configuring fftw-3.2.2; (may be time-consuming)" -+ # echo -+ # cd fftw-3.2.2 && \ -+ # env CC=3D"$cc" CFLAGS=3D"$cflags" ./configure $mdgxflag \ -+ # > ../fftw3_config.log 2>&1 -+ # ncerror=3D$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: fftw configure returned $ncerror" -+ # echo " fftw configure failed! Check the fftw3_config.log= file." -+ # exit 1 -+ # else -+ # echo " fftw-3.2.2 configure succeeded." -+ # fi -+ # cd .. -+ #fi -=20 - #--------------------------------------------------------------------= ------ - # Set up MPI 3D-RISM in NAB and SANDER -@@ -1307,23 +1307,23 @@ - echo - echo "Configuring fftw-2.1.5; (may be time-consuming)" - echo -- cd fftw-2.1.5 -- if [ "$mpi" =3D 'yes' ]; then -- ./configure $rismflag --enable-mpi CC=3D"$cc" CFLAGS=3D"$= cflags" F77=3D"$fc" FFLAGS=3D"$fflags" \ -- > ../fftw2_config.log 2>&1 -- else -- ./configure $rismflag CC=3D"$cc" CFLAGS=3D"$cflags" F77=3D= "$fc" FFLAGS=3D"$fflags" \ -- > ../fftw2_config.log 2>&1 -- fi -- ncerror=3D$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: fftw configure returned $ncerror" -- echo " fftw configure failed! Check the fftw2_config.= log file." -- exit 1 -- else -- echo " fftw-2.1.5 configure succeeded." -- fi -- cd .. -+ # cd fftw-2.1.5 -+ # if [ "$mpi" =3D 'yes' ]; then -+ # ./configure $rismflag --enable-mpi CC=3D"$cc" CFLAGS=3D"= $cflags" F77=3D"$fc" FFLAGS=3D"$fflags" \ -+ # > ../fftw2_config.log 2>&1 -+ # else -+ # ./configure $rismflag CC=3D"$cc" CFLAGS=3D"$cflags" F77=3D= "$fc" FFLAGS=3D"$fflags" \ -+ # > ../fftw2_config.log 2>&1 -+ # fi -+ # ncerror=3D$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: fftw configure returned $ncerror" -+ # echo " fftw configure failed! Check the fftw2_config= .log file." -+ # exit 1 -+ # else -+ # echo " fftw-2.1.5 configure succeeded." -+ # fi -+ # cd .. - flibs_fftw2=3D"\$(LIBDIR)/libdrfftw.a \$(LIBDIR)/libdfftw.a" - if [ "$mpi" =3D 'yes' ]; then - flibs_fftw2=3D"\$(LIBDIR)/libdrfftw_mpi.a \$(LIBDIR)/libd= fftw_mpi.a $flibs_fftw2" -diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Ma= kefile ---- amber11.orig/AmberTools/src/Makefile 2010-04-14 17:36:31.000000000 += 0400 -+++ amber11/AmberTools/src/Makefile 2011-03-07 03:39:38.000000000 +0300 -@@ -8,15 +8,15 @@ -=20 - install: serial -=20 --serial: configured_serial $(NETCDFLIB) -+serial: configured_serial - @echo "Starting installation of ${AMBERTOOLS} serial at `date`". - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - (cd etc && $(MAKE) install ) - (cd chamber && $(MAKE) install ) - (cd pbsa && $(MAKE) install ) -@@ -30,14 +30,14 @@ - (cd ptraj && $(MAKE) install ) -=20 - # miscellaneous: -- (cd reduce && $(MAKE) install ) -+# (cd reduce && $(MAKE) install ) -=20 - # leap and gleap: - (cd leap && $(MAKE) install ) - (cd gleap && $(MAKE) install ) -=20 - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd nab && $(MAKE) install ) - (cd nss && $(MAKE) install ) -=20 -@@ -50,15 +50,15 @@ -=20 - nabonly: $(NETCDFLIB)=20 - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -=20 - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd nab && $(MAKE) install ) - (cd nss && $(MAKE) install ) -=20 -diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/s= rc/pbsa/Makefile ---- amber11.orig/AmberTools/src/pbsa/Makefile 2010-04-14 17:26:17.000000= 000 +0400 -+++ amber11/AmberTools/src/pbsa/Makefile 2011-03-07 03:39:15.000000000 += 0300 -@@ -47,10 +47,10 @@ - $(LIBDIR)/libpbsa.a $(LIBDIR)/libFpbsa.a -=20 - #----------------------------------------------------------------------= ----- --pbsa$(SFX): $(OBJ) syslib netlib c9x-complex -+pbsa$(SFX): $(OBJ) syslib - $(FC) -o pbsa$(SFX) $(OBJ) ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS) -=20 --simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9= x-complex -+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib - $(FC) -o simplepbsa$(SFX) simplepbsa.o gopt.o libpbsa.a \ - $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) $(LDFLAGS) - /bin/mv simplepbsa$(SFX) $(BINDIR) -@@ -76,15 +76,15 @@ - sfflib: - cd ../sff && $(MAKE) install -=20 --netlib:=20 -- cd ../lapack && $(MAKE) $(LAPACK) -- cd ../blas && $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -- --c9x-complex: -- @if test $(C9XCOMPLEX) !=3D "skip"; then \ -- cd ../c9x-complex && $(MAKE) libmc.a; \ -- fi -+#netlib:=20 -+# cd ../lapack && $(MAKE) $(LAPACK) -+# cd ../blas && $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install -+ -+#c9x-complex: -+# @if test $(C9XCOMPLEX) !=3D "skip"; then \ -+# cd ../c9x-complex && $(MAKE) libmc.a; \ -+# fi -=20 - %.LIBPBSA.o: %.f - $(FPP) -DLIBPBSA $< > _$< -diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/= src/ptraj/Makefile ---- amber11.orig/AmberTools/src/ptraj/Makefile 2010-03-31 07:05:16.00000= 0000 +0400 -+++ amber11/AmberTools/src/ptraj/Makefile 2011-03-07 03:39:16.000000000 = +0300 -@@ -60,20 +60,20 @@ - rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) - $(CC) $(LDFLAGS) -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) -=20 --ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) -+ptraj$(SFX): libs $(NETCDFLIB) $(OBJECTS) - $(CC) $(LDFLAGS) -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) -=20 --ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) -+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) - $(CC) $(LDFLAGS) -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $= (LM) - # -=20 - libs:=20 - cd pdb && $(MAKE)=20 -- cd ../arpack && $(MAKE) -+# cd ../arpack && $(MAKE) -=20 --netlib: -- cd ../lapack; $(MAKE) $(LAPACK) -- cd ../blas; $(MAKE) $(BLAS) -+#netlib: -+# cd ../lapack; $(MAKE) $(LAPACK) -+# cd ../blas; $(MAKE) $(BLAS) -=20 - clean: - cd pdb; $(MAKE) clean -diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/Amber= Tools/src/ptraj/netcdf_ptraj.h ---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2010-03-31 07:05:16= .000000000 +0400 -+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-03-07 03:39:17.0000= 00000 +0300 -@@ -4,7 +4,7 @@ - # include "../pnetcdf/include/pnetcdf.h" - # define nc_strerror ncmpi_strerror - # else --# include "../netcdf/include/netcdf.h" -+# include - # endif=20 - #endif -=20 -diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/s= rc/ptraj/ptraj.h ---- amber11.orig/AmberTools/src/ptraj/ptraj.h 2010-03-31 07:05:16.000000= 000 +0400 -+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-03-07 03:39:17.000000000 += 0300 -@@ -94,7 +94,7 @@ - #define nc_strerror ncmpi_strerror - #include "../pnetcdf/include/pnetcdf.h" - #else --#include "../netcdf/include/netcdf.h" -+#include - #endif - #endif -=20 -diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/sr= c/sqm/Makefile ---- amber11.orig/AmberTools/src/sqm/Makefile 2010-04-14 16:13:28.0000000= 00 +0400 -+++ amber11/AmberTools/src/sqm/Makefile 2011-03-07 03:39:17.000000000 +0= 300 -@@ -77,7 +77,7 @@ - install: sqm$(SFX) - mv sqm$(SFX) $(BINDIR) -=20 --sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys -+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys - $(FC) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) $(FLIBSF) ../lib/sys.a $(LDFLAGS= ) -=20 - #-----------LIBS -@@ -93,10 +93,10 @@ - sys: - cd ../lib; $(MAKE) sys.a -=20 --netlib: -- cd ../lapack; $(MAKE) $(LAPACK) -- cd ../blas; $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -+#netlib: -+# cd ../lapack; $(MAKE) $(LAPACK) -+# cd ../blas; $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install -=20 - clean: - /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b= /sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch deleted file mode 100644 index 0e41d26..0000000 --- a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch +++ /dev/null @@ -1,386 +0,0 @@ -diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/c= onfigure ---- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 = +0300 -+++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300 -@@ -293,7 +293,8 @@ - echo "Your AMBERHOME environment variable is not set! It should be s= et to" - echo "$ambhome NOT doing so may cause errors when you compile. Cont= inue" - echo "anyway? (yes or no)" -- read answer -+ #read answer -+ answer=3D'yes' - if [ "$answer" =3D 'yes' -o "$answer" =3D 'Yes' -o "$answer" =3D 'YE= S' -o "$answer" =3D 'y' -o "$answer" =3D 'Y' ]; then - echo "" - echo "Continuing anyway... Setting AMBERHOME to $ambhome temporar= ily" -@@ -356,11 +357,11 @@ - mpi_flag=3D - lex=3Dflex - flibs_mkl=3D --lapack=3Dinstall --blas=3Dinstall -+lapack=3Dskip -+blas=3Dskip - f2c=3Dskip --ucpp=3Dinstall --cpp=3D"\$(BINDIR)/ucpp -l" -+ucpp=3Dskip -+cpp=3D"\$(EPREFIX)/usr/bin/ucpp -l" -=20 - #----------------------------------- - # skip building of sleap? -@@ -1655,24 +1656,24 @@ - #--------------------------------------------------------------------= ------ - # Configure fftw-3.2.2: - #--------------------------------------------------------------------= ------ -- if [ "$mdgx" =3D 'yes' ]; then -- mdgxflag=3D"--prefix=3D$AMBERHOME --disable-fortran"=20 -- echo -- echo "Configuring fftw-3.2.2 (may be time-consuming)..." -- echo -- cd fftw-3.2.2 && \ -- env CC=3D"$cc" CFLAGS=3D"$cflags $cnooptflags" \ -- ./configure $mdgxflag > ../fftw3_config.log 2>&1 -- ncerror=3D$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: FFTW configure returned $ncerror" -- echo " FFTW configure failed! Check the fftw3_config.log f= ile." -- exit 1 -- else -- echo " fftw-3.2.2 configure succeeded." -- fi -- cd .. -- fi -+ #if [ "$mdgx" =3D 'yes' ]; then -+ # mdgxflag=3D"--prefix=3D$AMBERHOME --disable-fortran"=20 -+ # echo -+ # echo "Configuring fftw-3.2.2 (may be time-consuming)..." -+ # echo -+ # cd fftw-3.2.2 && \ -+ # env CC=3D"$cc" CFLAGS=3D"$cflags $cnooptflags" \ -+ # ./configure $mdgxflag > ../fftw3_config.log 2>&1 -+ # ncerror=3D$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: FFTW configure returned $ncerror" -+ # echo " FFTW configure failed! Check the fftw3_config.log = file." -+ # exit 1 -+ # else -+ # echo " fftw-3.2.2 configure succeeded." -+ # fi -+ # cd .. -+ #fi -=20 - #--------------------------------------------------------------------= ------ - # Configure python -@@ -1792,27 +1793,27 @@ - echo - echo "Configuring fftw-2.1.5 (may be time-consuming)..." - echo -- cd fftw-2.1.5 -- if [ "$mpi" =3D 'yes' ]; then -- ./configure $rismflag --enable-mpi \ -- CC=3D"$cc" CFLAGS=3D"$cflags $coptflags" \ -- F77=3D"$fc" FFLAGS=3D"$fflags $foptflags" \ -- FLIBS=3D"$flibs_arch" > ../fftw2_config.log 2>&1 -- else -- ./configure $rismflag \ -- CC=3D"$cc" CFLAGS=3D"$cflags $coptflags" \ -- F77=3D"$fc" FFLAGS=3D"$fflags $foptflags" \ -- FLIBS=3D"$flibs_arch" > ../fftw2_config.log 2>&1 -- fi -- ncerror=3D$? -- if [ $ncerror -gt 0 ]; then -- echo " Error: fftw configure returned $ncerror" -- echo " fftw configure failed! Check the fftw2_config.= log file." -- exit 1 -- else -- echo " fftw-2.1.5 configure succeeded." -- fi -- cd .. -+ # cd fftw-2.1.5 -+ # if [ "$mpi" =3D 'yes' ]; then -+ # ./configure $rismflag --enable-mpi \ -+ # CC=3D"$cc" CFLAGS=3D"$cflags $coptflags" \ -+ # F77=3D"$fc" FFLAGS=3D"$fflags $foptflags" \ -+ # FLIBS=3D"$flibs_arch" > ../fftw2_config.log 2>&1 -+ # else -+ # ./configure $rismflag \ -+ # CC=3D"$cc" CFLAGS=3D"$cflags $coptflags" \ -+ # F77=3D"$fc" FFLAGS=3D"$fflags $foptflags" \ -+ # FLIBS=3D"$flibs_arch" > ../fftw2_config.log 2>&1 -+ # fi -+ # ncerror=3D$? -+ # if [ $ncerror -gt 0 ]; then -+ # echo " Error: fftw configure returned $ncerror" -+ # echo " fftw configure failed! Check the fftw2_config= .log file." -+ # exit 1 -+ # else -+ # echo " fftw-2.1.5 configure succeeded." -+ # fi -+ # cd .. - flibs_fftw2=3D"-ldrfftw -ldfftw" - if [ "$mpi" =3D 'yes' ]; then - flibs_fftw2=3D"-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2" -diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/Am= berTools/src/cpptraj/src/Makefile_at ---- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30= :16.000000000 +0300 -+++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.0= 00000000 +0300 -@@ -65,8 +65,8 @@ - -/bin/rm FindDepend.o - -/bin/rm findDepend -=20 --cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS) -- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(B= ZLIB) -+cpptraj$(SFX): $(OBJECTS) -+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(B= ZLIB) -lgomp -=20 - $(NETCDFLIB): ../../netcdf_config.log - cd ../../netcdf/src && $(MAKE) install -diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Ma= kefile ---- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 += 0300 -+++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300 -@@ -8,15 +8,15 @@ -=20 - install: $(INSTALLTYPE) -=20 --serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP) -+serial: configured_serial - @echo "Starting installation of ${AMBERTOOLS} serial at `date`". - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - (cd etc && $(MAKE) install ) - (cd chamber && $(MAKE) install ) - (cd pbsa && $(MAKE) install ) -@@ -32,7 +32,7 @@ - (cd cpptraj && $(MAKE) $(CPPTRAJ)) -=20 - # miscellaneous: -- (cd reduce && $(MAKE) install ) -+# (cd reduce && $(MAKE) install ) -=20 - # leap and gleap: - (cd leap && $(MAKE) install ) -@@ -42,7 +42,7 @@ - (cd rism && $(MAKE) install ) -=20 - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd sff && $(MAKE) install ) - (cd pbsa && $(MAKE) libinstall ) - (cd nab && $(MAKE) install ) -@@ -63,19 +63,19 @@ - @echo "Installation of ${AMBERTOOLS} serial is complete at `date`." - @echo "" -=20 --nabonly: $(NETCDFLIB)=20 -+nabonly: - # utility routines and libraries: -- (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -+# (cd ucpp-1.3 && $(MAKE) $(UCPP) ) - (cd byacc && $(MAKE) install ) -- (cd arpack && $(MAKE) install ); -- (cd lapack && $(MAKE) $(LAPACK) ) -- (cd blas && $(MAKE) $(BLAS) ) -- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) -+# (cd arpack && $(MAKE) install ); -+# (cd lapack && $(MAKE) $(LAPACK) ) -+# (cd blas && $(MAKE) $(BLAS) ) -+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) ) - (cd pbsa && $(MAKE) libinstall ) - (cd rism && $(MAKE) install ) -=20 - # nab: -- (cd cifparse && $(MAKE) install ) -+# (cd cifparse && $(MAKE) install ) - (cd sff && $(MAKE) install ) - (cd nab && $(MAKE) install ) - (cd nss && $(MAKE) install ) -diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/s= rc/mdgx/Makefile ---- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000= 000 +0300 -+++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 += 0300 -@@ -109,7 +109,7 @@ -=20 - FFTW_LIBS =3D $(LIBDIR)/libfftw3.a -=20 --mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) -+mdgx$(SFX) : $(MDGX_OBJS) - $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ - -o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM) -=20 -diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/s= rc/pbsa/Makefile ---- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000= 000 +0300 -+++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 += 0300 -@@ -148,7 +148,7 @@ - ) -=20 - #----------------------------------------------------------------------= ----- --pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial -+pbsa$(SFX): $(OBJ) syslib configured_serial - $(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \ - ../lib/nxtsec.o ../lib/random.o \ - $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) -@@ -158,7 +158,7 @@ - ../lib/nxtsec.o ../lib/random.o \ - $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS) -=20 --simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9= x-complex -+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib - $(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o= \ - libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \ - $(LDFLAGS) $(AMBERLDFLAGS) -@@ -194,15 +194,15 @@ - sfflib: - cd ../sff && $(MAKE) install -=20 --netlib:=20 -- cd ../lapack && $(MAKE) $(LAPACK) -- cd ../blas && $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -- --c9x-complex: -- @if test $(C9XCOMPLEX) !=3D "skip"; then \ -- cd ../c9x-complex && $(MAKE) libmc.a; \ -- fi -+#netlib:=20 -+# cd ../lapack && $(MAKE) $(LAPACK) -+# cd ../blas && $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install -+ -+#c9x-complex: -+# @if test $(C9XCOMPLEX) !=3D "skip"; then \ -+# cd ../c9x-complex && $(MAKE) libmc.a; \ -+# fi -=20 - %.LIBPBSA.o: %.f - $(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$< -diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/= src/ptraj/Makefile ---- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.00000= 0000 +0300 -+++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 = +0300 -@@ -57,25 +57,25 @@ - pubfft.o: pubfft.f - $(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $= @ $< -=20 --rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS) -+rdparm$(SFX): libs $(OBJECTS) - $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ - -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) -=20 --ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS) -+ptraj$(SFX): libs $(OBJECTS) - $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ - -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM) -=20 --ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS) -+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS) - $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ - -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM) -=20 - libs:=20 - cd pdb && $(MAKE)=20 -- cd ../arpack && $(MAKE) -+# cd ../arpack && $(MAKE) -=20 --netlib: -- cd ../lapack && $(MAKE) $(LAPACK) -- cd ../blas && $(MAKE) $(BLAS) -+#netlib: -+# cd ../lapack && $(MAKE) $(LAPACK) -+# cd ../blas && $(MAKE) $(BLAS) -=20 - clean: - cd pdb && $(MAKE) clean -diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/Amber= Tools/src/ptraj/netcdf_ptraj.h ---- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19= .000000000 +0300 -+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.0000= 00000 +0300 -@@ -4,7 +4,7 @@ - # include "../../include/pnetcdf.h" - # define nc_strerror ncmpi_strerror - # else --# include "../../include/netcdf.h" -+# include - # endif=20 - #endif -=20 -diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/s= rc/ptraj/ptraj.h ---- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000= 000 +0300 -+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 += 0300 -@@ -94,7 +94,7 @@ - #define nc_strerror ncmpi_strerror - #include "../../include/pnetcdf.h" - #else --#include "../../include/netcdf.h" -+#include - #endif - #endif -=20 -diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/s= rc/rism/Makefile ---- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000= 000 +0300 -+++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 += 0300 -@@ -49,7 +49,7 @@ - mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \ - fce_c.o erfcfun.o safemem.o blend.o timer_c.o -=20 --librism: $(LIBOBJ) $(FLIBS_FFTW2) -+librism: $(LIBOBJ) - $(AR) $(LIBDIR)/$@.a $(LIBOBJ) - $(RANLIB) $(LIBDIR)/$@.a -=20 -diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberToo= ls/src/sff/AmberNetcdf.c ---- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.00= 0000000 +0300 -+++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.0000000= 00 +0300 -@@ -27,7 +27,7 @@ - #endif - =20 - #ifdef BINTRAJ --#include "../../include/netcdf.h" -+#include -=20 - #define NCFRAME "frame" - #define NCSPATIAL "spatial" -diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/sr= c/sff/Makefile ---- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.0000000= 00 +0300 -+++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0= 300 -@@ -1,7 +1,7 @@ - include ../config.h -=20 - .c.o: -- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@= $< -+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NET= CDFLIB) -o $@ $< -=20 - OBJS =3D binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.= o \ - prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \ -diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/sr= c/sqm/Makefile ---- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.0000000= 00 +0300 -+++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0= 300 -@@ -77,7 +77,7 @@ - install: sqm$(SFX) - mv sqm$(SFX) $(BINDIR) -=20 --sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys -+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys - $(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \ - $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS) -=20 -@@ -94,10 +94,10 @@ - sys: - cd ../lib; $(MAKE) sys.a -=20 --netlib: -- cd ../lapack; $(MAKE) $(LAPACK) -- cd ../blas; $(MAKE) $(BLAS) -- cd ../arpack && $(MAKE) install -+#netlib: -+# cd ../lapack; $(MAKE) $(LAPACK) -+# cd ../blas; $(MAKE) $(BLAS) -+# cd ../arpack && $(MAKE) install -=20 - clean: - /bin/rm -f *.o _*.f *.mod *.d sqm$(SFX) diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambert= ools/metadata.xml deleted file mode 100644 index 20e218e..0000000 --- a/sci-chemistry/ambertools/metadata.xml +++ /dev/null @@ -1,10 +0,0 @@ - - - - sci-chemistry - - alexxy@gentoo.org - Alexey Shvetsov - - -