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authorJustin Lecher <jlec@gentoo.org>2011-08-30 13:48:39 +0000
committerJustin Lecher <jlec@gentoo.org>2011-08-30 13:48:39 +0000
commit2a2c84e4fcdcc697697ceb0031920a13e990ebd5 (patch)
tree439511b0d8db8eb94ffe6603d7080448663bf6a8 /sci-chemistry/cns
parentChange version scheme (diff)
downloadgentoo-2-2a2c84e4fcdcc697697ceb0031920a13e990ebd5.tar.gz
gentoo-2-2a2c84e4fcdcc697697ceb0031920a13e990ebd5.tar.bz2
gentoo-2-2a2c84e4fcdcc697697ceb0031920a13e990ebd5.zip
Bump patches to aria-2.3.2
(Portage version: 2.2.0_alpha51/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry/cns')
-rw-r--r--sci-chemistry/cns/ChangeLog8
-rw-r--r--sci-chemistry/cns/cns-1.2.1-r7.ebuild243
-rw-r--r--sci-chemistry/cns/metadata.xml14
3 files changed, 257 insertions, 8 deletions
diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index a0236a7f6a9f..1bd239e64d35 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,12 @@
# ChangeLog for sci-chemistry/cns
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.41 2011/06/21 16:05:16 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.42 2011/08/30 13:48:39 jlec Exp $
+
+*cns-1.2.1-r7 (30 Aug 2011)
+
+ 30 Aug 2011; Justin Lecher <jlec@gentoo.org> +cns-1.2.1-r7.ebuild,
+ metadata.xml:
+ Bump patches to aria-2.3.2
21 Jun 2011; Justin Lecher <jlec@gentoo.org> cns-1.1.ebuild,
cns-1.2.1.ebuild, cns-1.2.1-r5.ebuild, cns-1.2.1-r6.ebuild,
diff --git a/sci-chemistry/cns/cns-1.2.1-r7.ebuild b/sci-chemistry/cns/cns-1.2.1-r7.ebuild
new file mode 100644
index 000000000000..64faf0bedc57
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r7.ebuild
@@ -0,0 +1,243 @@
+# Copyright 1999-2011 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-r7.ebuild,v 1.1 2011/08/30 13:48:39 jlec Exp $
+
+EAPI=3
+
+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="
+ ${MY_P}_all-mp.tar.gz
+ aria? ( aria2.3.2.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="
+ virtual/fortran
+ app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+FORTRAN_NEED_OPENMP=1
+
+S="${WORKDIR}/${MY_P}"
+
+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 "in ${DISTDIR}."
+}
+
+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/
+ 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 "${T}"/
+ sed -i \
+ -e "s:_CNSsolve_location_:${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 [[ $(tc-getFC) =~ g77 ]]; then
+ GLOBALS="-fno-globals"
+ MALIGN='\$(CNS_MALIGN_I86)'
+ fi
+
+ # Set up the compiler to use
+ pushd instlib/machine/unsupported/g77-unix 2>/dev/null
+ ln -s Makefile.header Makefile.header.${FCOMP} || 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="$(tc-getCC)" \
+ F77=$(tc-getFC) \
+ LD=$(tc-getFC) \
+ CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+ LDFLAGS="${LDFLAGS}" \
+ F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
+ F77STD="${GLOBALS}" \
+ OMPLIB="${OMPLIB}" \
+ compiler="${COMP}" \
+ install \
+ || 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/${PF}:g" \
+ -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
+ -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+ -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+ -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+ -e "/^g77on/d" \
+ "${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/${PF}:g" \
+ -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
+ -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
+ -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
+ -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+ -e "/^g77on/d" \
+ -e "/^g77off/d" \
+ "${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}"/*linux*/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 "${S}"/*linux*/utils/Makefile
+
+ dobin "${S}"/*linux*/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 "${T}"/cns_solve_env_sh cns_solve_env.sh || die
+
+ dohtml \
+ -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
+ -f all_cns_info_template,omac,def \
+ -r doc/html/* || die
+ # Conflits with app-text/dos2unix
+ rm -f "${D}"/usr/bin/dos2unix
+}
+
+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
+}
diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml
index 9d53ac3f3a11..3fbfefd30233 100644
--- a/sci-chemistry/cns/metadata.xml
+++ b/sci-chemistry/cns/metadata.xml
@@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci-chemistry</herd>
-<maintainer>
- <email>jlec@gentoo.org</email>
-</maintainer>
-<use>
- <flag name='aria'> Support patch for sci-chemistry/aria</flag>
-</use>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+ <use>
+ <flag name="aria"> Support patch for sci-chemistry/aria</flag>
+ </use>
</pkgmetadata>