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-rw-r--r--profiles/package.mask5
-rw-r--r--sci-chemistry/ambertools/Manifest7
-rw-r--r--sci-chemistry/ambertools/ambertools-1.2.ebuild92
-rw-r--r--sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch42
-rw-r--r--sci-chemistry/ambertools/files/1.2-Makefile_at.patch32
-rw-r--r--sci-chemistry/ambertools/files/1.2-configure_at.patch29
-rw-r--r--sci-chemistry/ambertools/files/1.2-f2c.patch36
-rw-r--r--sci-chemistry/ambertools/metadata.xml8
8 files changed, 0 insertions, 251 deletions
diff --git a/profiles/package.mask b/profiles/package.mask
index 0ed44f6d2..7b0f94c61 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -44,8 +44,3 @@
# jlec@j-schmitz.net
# total rewrite of src_install
=sci-libs/cctbx-2009.02.15.2320-r2
-
-# Justin Lecher (jlec) (23 Mar 09)
-# jlec@j-schmitz.net
-# still some issues
-=sci-chemistry/ambertools-1.2
diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest
deleted file mode 100644
index edda052d0..000000000
--- a/sci-chemistry/ambertools/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX 1.2-Makefile_at-f2c.patch 1169 RMD160 114ed61db0bc5759cdce0501252ccf68525f05c8 SHA1 ce3742a65ddb3472d38ac3265bf9ae0de64ef21c SHA256 6d1f4de9d7a7e8826f5acbf6ee4aee5c0dd10596e25e51b229c7975e6dc71bfa
-AUX 1.2-Makefile_at.patch 830 RMD160 610311006a6d5ed95aedb81ecf1bb849c1dd3bdd SHA1 34d7e60d33196b0f3abc357ee965a179ec1c0581 SHA256 bbd7f96be1638d55c8171077e21474c1a98a300c03e367b18bdc8555e40e9745
-AUX 1.2-configure_at.patch 853 RMD160 cd50792ce60f2537d121ebd8531b3bb70539ba95 SHA1 d632b90a7c525e1b7636d713a119316a38e3903e SHA256 58c009dae95aa4f60b2f6423f3794e4c8491f423f2df2d30e9606f0b2842d458
-AUX 1.2-f2c.patch 1012 RMD160 78e0c5a5320f151e031f5c546d88292ece0852c8 SHA1 5a2f98686e5e0444ab0505cb4c0cba97ac0f4332 SHA256 f857a9b972e54803a5684511708a273c0c895a41a4dbbfac9c168900968d618d
-DIST AmberTools-1.2.tar.bz2 50621801 RMD160 01dd22dd86b90148111dc0616964384dfeda467c SHA1 001db6742fdbf0f0f8c862d1b08a59ea3da0b684 SHA256 1630e0c0135de05441226a08a5f60d861faeb7a06f5d1a4bc38e9eeff4b2f991
-EBUILD ambertools-1.2.ebuild 2374 RMD160 58858e7c056bda4c973e4f227dcacb3427203c8e SHA1 cac33fc2cba08464d18d188d54d8263b03c69953 SHA256 a8c50224588cf987e1f4aa5148f6bbfb78d57b0af4d695753959585024893468
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/ambertools/ambertools-1.2.ebuild b/sci-chemistry/ambertools/ambertools-1.2.ebuild
deleted file mode 100644
index 15e5e2741..000000000
--- a/sci-chemistry/ambertools/ambertools-1.2.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit toolchain-funcs eutils fortran
-
-FORTRAN="g77 gfortran ifc"
-
-DESCRIPTION="A suite of programs for carrying out complete molecular mechanics investigations"
-HOMEPAGE="http://ambermd.org/#AmberTools"
-SRC_URI="AmberTools-${PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi openmp scalapack X"
-RESTRICT="fetch"
-
-RDEPEND="virtual/cblas
- sci-libs/clapack
- sci-libs/cifparse-obj
- sci-chemistry/mopac7
- sci-libs/netcdf
- sci-chemistry/reduce"
-DEPEND="${RDEPEND}
- dev-util/byacc
- dev-libs/libf2c
- sys-devel/ucpp"
-S="${WORKDIR}"/amber10
-
-pkg_nofetch() {
- einfo "Go to ${HOMEPAGE} and get ${A}"
- einfo "Place it in ${DISTDIR}"
-}
-
-pkg_setup() {
- need_fortran "${FORTRAN}"
- if use openmp &&
- [[ $(tc-getCC)$ == *gcc* ]] &&
- ( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] ||
- ! built_with_use sys-devel/gcc openmp )
- then
- ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 "
- ewarn "If you want to build ${PN} with OpenMP, abort now,"
- ewarn "and switch CC to an OpenMP capable compiler"
- fi
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/${PV}-configure_at.patch \
- "${FILESDIR}"/${PV}-Makefile_at.patch
-# "${FILESDIR}"/${PV}-Makefile_at-f2c.patch
-# "${FILESDIR}"/${PV}-f2c.patch
- cd src && rm -rf byacc c9x-complex carpack cblas cifparse clapack mopac6 netcdf reduce ucpp-1.3
-# f2c
-}
-
-src_configure() {
- cd src
- sed -e "s:\\\\\$(LIBDIR)/arpack.a:/usr/$(get_libdir)/libarpack.a:g" \
- -e "s:\\\\\$(LIBDIR)/lapack.a:/usr/$(get_libdir)/libclapack.a:g" \
- -e "s:\\\\\$(LIBDIR)/blas.a:/usr/$(get_libdir)/libcblas.a:g" \
- -e "s:\\\\\$(LIBDIR)/f2c.a:/usr/$(get_libdir)/libf2c.a:g" \
- -e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
- -e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
- -e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
- -e "s:fc=g77:fc=${FORTRANC}:g" \
- -e "s:NETCDFLIB=\$netcdflib:NETCDFLIB=/usr/$(get_libdir)/libnetcdf.a:g" \
- -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
- -e "s:-O3::g" \
- -i configure_at
-
- local myconf
-
- use X || myconf="${myconf} -noX11"
-
- for x in mpi openmp scalapack; do
- use ${x} && myconf="${myconf} -${x}"
- done
-
- ./configure_at \
- ${myconf} \
- -nobintraj \
- $(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-}
-
-src_compile() {
- cd src
- emake -f Makefile_at || die
-}
diff --git a/sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch b/sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch
deleted file mode 100644
index a5da04962..000000000
--- a/sci-chemistry/ambertools/files/1.2-Makefile_at-f2c.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- src/Makefile_at 2008-07-11 00:09:01.000000000 +0200
-+++ src/Makefile_at.new 2009-03-25 15:35:51.000000000 +0100
-@@ -5,29 +5,29 @@
- install:
- -mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
- # utility routines and libraries:
-- (cd ucpp-1.3 && make $(UCPP) )
-- (cd byacc && make install )
-- (cd carpack && make install );
-- (cd clapack && make $(LAPACK) )
-- (cd cblas && make $(BLAS) )
-- (cd f2c && make $(F2C) )
-- (cd c9x-complex && make $(C9XCOMPLEX) )
-+# (cd ucpp-1.3 && make $(UCPP) )
-+# (cd byacc && make install )
-+# (cd carpack && make install );
-+# (cd clapack && make $(LAPACK) )
-+# (cd cblas && make $(BLAS) )
-+# (cd f2c && make $(F2C) )
-+# (cd c9x-complex && make $(C9XCOMPLEX) )
-
- # nab, leap, and sleap:
-- (cd cifparse && make install )
-+# (cd cifparse && make install )
- (cd nab && make install )
- (cd nss && make install )
-
- # antechamber:
- (cd antechamber && make install )
-- (cd mopac6/src && make $(G77) )
-+# (cd mopac6/src && make $(G77) )
- (cd resp && make $(G77) )
-
- # ptraj:
- (cd ptraj && make install )
-
- # miscellaneous:
-- (cd reduce && make install )
-+# (cd reduce && make install )
-
- # leap and gleap:
- (cd leap && make install )
diff --git a/sci-chemistry/ambertools/files/1.2-Makefile_at.patch b/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
deleted file mode 100644
index 139f04e8c..000000000
--- a/sci-chemistry/ambertools/files/1.2-Makefile_at.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- src/Makefile_at 2008-07-11 00:09:01.000000000 +0200
-+++ src/Makefile_at.new 2009-03-25 19:05:35.000000000 +0100
-@@ -5,29 +5,20 @@
- install:
- -mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
- # utility routines and libraries:
-- (cd ucpp-1.3 && make $(UCPP) )
-- (cd byacc && make install )
-- (cd carpack && make install );
-- (cd clapack && make $(LAPACK) )
-- (cd cblas && make $(BLAS) )
- (cd f2c && make $(F2C) )
-- (cd c9x-complex && make $(C9XCOMPLEX) )
-
- # nab, leap, and sleap:
-- (cd cifparse && make install )
- (cd nab && make install )
- (cd nss && make install )
-
- # antechamber:
- (cd antechamber && make install )
-- (cd mopac6/src && make $(G77) )
- (cd resp && make $(G77) )
-
- # ptraj:
- (cd ptraj && make install )
-
- # miscellaneous:
-- (cd reduce && make install )
-
- # leap and gleap:
- (cd leap && make install )
diff --git a/sci-chemistry/ambertools/files/1.2-configure_at.patch b/sci-chemistry/ambertools/files/1.2-configure_at.patch
deleted file mode 100644
index 9c409462f..000000000
--- a/sci-chemistry/ambertools/files/1.2-configure_at.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- src/configure_at 2009-03-22 20:55:51.394457545 +0100
-+++ src/configure_at.new 2009-03-22 20:50:01.155363408 +0100
-@@ -163,7 +163,7 @@
- blas=install
- f2c=install
- ucpp=install
--cpp="\$(BINDIR)/ucpp -l"
-+cpp="/usr/bin/ucpp -l"
-
- #-----------------------------------
- # skip building of sleap?
-@@ -501,7 +501,7 @@
- echo ""
- echo "Obtaining the C++ compiler version:"
- echo " $cplusplus -v"
-- version=`$cplusplus -v 2>&1 | grep version | cut -d' ' -f3`
-+ version=`$cplusplus -v 2>&1 | grep " version " | cut -d' ' -f3`
- echo "The version is $version"
- majorversion=`echo $version | cut -d'.' -f1`
- minorversion=`echo $version | cut -d'.' -f2`
-@@ -698,7 +698,7 @@
- LDFLAGS=$ldflags
-
- LEX= $lex
--YACC= \$(BINDIR)/yacc
-+YACC= /usr/bin/byacc
- AR= ar rv
- M4= $m4
- RANLIB=$ranlib
diff --git a/sci-chemistry/ambertools/files/1.2-f2c.patch b/sci-chemistry/ambertools/files/1.2-f2c.patch
deleted file mode 100644
index a77d7f60c..000000000
--- a/sci-chemistry/ambertools/files/1.2-f2c.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-diff -arNu src/nab.orig/dmcsrch.c src/nab/dmcsrch.c
---- src/nab.orig/dmcsrch.c 2009-03-24 22:35:01.000000000 +0100
-+++ src/nab/dmcsrch.c 2009-03-24 22:35:05.000000000 +0100
-@@ -3,7 +3,7 @@
- -lf2c -lm (in that order)
- */
-
--#include "../f2c/f2c.h"
-+#include <f2c.h>
-
- /* Original version from Jorge Nocedal, slightly modified */
- /* by Istvan Kolossvary to link to libXMIN. See CIK comments. */
-diff -arNu src/nab.orig/ms.c src/nab/ms.c
---- src/nab.orig/ms.c 2009-03-24 22:35:01.000000000 +0100
-+++ src/nab/ms.c 2009-03-24 22:35:09.000000000 +0100
-@@ -3,7 +3,7 @@
- -lf2c -lm (in that order)
- */
-
--#include "../f2c/f2c.h"
-+#include <f2c.h>
-
- /* Common Block Declarations */
-
-diff -arNu src/nab.orig/nmode.c src/nab/nmode.c
---- src/nab.orig/nmode.c 2009-03-24 22:35:01.000000000 +0100
-+++ src/nab/nmode.c 2009-03-24 22:35:04.000000000 +0100
-@@ -7,7 +7,7 @@
- #else
- # include <complex.h>
- #endif
--#include "../f2c/f2c.h"
-+#include <f2c.h>
-
- #include "nab.h"
- #include "memutil.h"
diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/sci-chemistry/ambertools/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>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>