* [gentoo-commits] gentoo-x86 commit in sci-chemistry/cns: ChangeLog cns-1.2.1-r3.ebuild
@ 2010-03-20 13:33 Justin Lecher (jlec)
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From: Justin Lecher (jlec) @ 2010-03-20 13:33 UTC (permalink / raw
To: gentoo-commits
jlec 10/03/20 13:33:12
Modified: ChangeLog
Added: cns-1.2.1-r3.ebuild
Log:
Included new version of aria
(Portage version: 2.2_rc67/cvs/Linux x86_64)
Revision Changes Path
1.21 sci-chemistry/cns/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/ChangeLog?rev=1.21&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/ChangeLog?rev=1.21&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/ChangeLog?r1=1.20&r2=1.21
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- ChangeLog 7 Mar 2010 09:54:15 -0000 1.20
+++ ChangeLog 20 Mar 2010 13:33:12 -0000 1.21
@@ -1,6 +1,17 @@
# ChangeLog for sci-chemistry/cns
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.20 2010/03/07 09:54:15 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.21 2010/03/20 13:33:12 jlec Exp $
+
+ 20 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+ +files/1.2.1-aria2.3.patch, +cns-1.2.1-r3.ebuild,
+ +files/1.2.1-parallel.patch:
+ Included new version of aria
+
+*cns-1.2.1-r3 (20 Mar 2010)
+
+ 20 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+ +files/1.2.1-aria2.3.patch, +cns-1.2.1-r3.ebuild:
+ Bump to new aria-2.3
07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> cns-1.2.1-r2.ebuild:
Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me
1.1 sci-chemistry/cns/cns-1.2.1-r3.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r3.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r3.ebuild?rev=1.1&content-type=text/plain
Index: cns-1.2.1-r3.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r3.ebuild,v 1.1 2010/03/20 13:33:12 jlec Exp $
EAPI="3"
inherit eutils fortran 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="${MY_P}_all-mp.tar.gz
aria? ( aria2.3.1.tar.gz )"
SLOT="0"
LICENSE="cns"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="aria openmp"
RDEPEND="app-shells/tcsh
!app-text/dos2unix"
DEPEND="${RDEPEND}"
PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )"
RESTRICT="fetch"
S="${WORKDIR}/${MY_P}"
FORTRAN="g77 gfortran"
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 "in ${DISTDIR}."
}
pkg_setup() {
fortran_pkg_setup
if [[ $(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 "Switch CC to an OpenMP capable compiler"
fi
}
src_prepare() {
epatch "${FILESDIR}"/${PV}-gentoo.patch
epatch "${FILESDIR}"/${PV}-parallel.patch
pushd "${WORKDIR}"/aria* >& /dev/null
if use aria; then
# Update the cns sources in aria for version 1.2.1
epatch "${FILESDIR}"/1.2.1-aria2.3.patch
# Update the code with aria specific things
cp -rf cns/src/* "${S}"/source/
fi
popd >& /dev/null
use openmp && append-fflags -fopenmp
# the code uses Intel-compiler-specific directives
epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
use openmp && OMPLIB="-lgomp"
use amd64 && \
append-cflags "-DINTEGER='long long int'" && \
append-fflags -fdefault-integer-8
# Set up location for the build directory
# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
sed -i \
-e "s:_CNSsolve_location_:${S}:g" \
-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
"${S}"/cns_solve_env
sed -i \
-e "s:_CNSsolve_location_:${S}:g" \
-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
"${T}"/cns_solve_env_sh
einfo "Fixing shebangs..."
find "${S}" -type f \
-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
}
src_compile() {
local GLOBALS
local MALIGN
if [[ ${FORTRANC} = g77 ]]; then
GLOBALS="-fno-globals"
MALIGN='\$(CNS_MALIGN_I86)'
fi
# Set up the compiler to use
pushd instlib/machine/unsupported/g77-unix 2>/dev/null
ln -s Makefile.header Makefile.header.${FORTRANC} || die
popd 2>/dev/null
# 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="$(tc-getCC)" \
F77="${FORTRANC}" \
LD="${FORTRANC}" \
CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
LDFLAGS="${LDFLAGS}" \
F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
F77STD="${GLOBALS}" \
OMPLIB="${OMPLIB}" \
g77install \
|| die "emake failed"
}
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() {
# Install to locations resembling FHS
sed -i \
-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/${PF}:g" \
-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
"${S}"/cns_solve_env
# I don't entirely understand why the sh version requires a leading /
# for CNS_SOLVE and CNS_ROOT, but it does
sed -i \
-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/${PF}:g" \
-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
"${T}"/cns_solve_env_sh
# Get rid of setup stuff we don't need in the installed script
sed -i \
-e "83,$ d" \
-e "37,46 d" \
"${S}"/cns_solve_env
sed -i \
-e "84,$ d" \
-e "39,50 d" \
"${T}"/cns_solve_env_sh
newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
|| die "install cns_solve failed"
# Can be run by either cns_solve or cns
dosym cns_solve /usr/bin/cns
# Don't want to install this
rm -f "${S}"/*_g77/utils/Makefile
dobin "${S}"/*_g77/utils/* || die "install utils failed"
sed -i \
-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
"${S}"/bin/cns_web || die
dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
insinto /usr/share/cns
doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
doins "${S}"/bin/cns_info || die
insinto /etc/profile.d
newins "${S}"/cns_solve_env cns_solve_env.csh || die
newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
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/* || die
}
pkg_info() {
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
}
pkg_postinst() {
pkg_info
}
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