Add CNS, an important package in X-ray crystallography and nuclear magnetic resonance (NMR).

Package-Manager: portage-2.1_rc4-r3

6 files changed, 188 insertions, 0 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
new file mode 100644
index 000000000000..e551299ef8d1
--- /dev/null
+++ b/sci-chemistry/cns/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/cns
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.1 2006/06/10 07:28:49 spyderous Exp $
+
+*cns-1.1 (10 Jun 2006)
+
+  10 Jun 2006; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/1.1-time-length-10.patch, +metadata.xml, +cns-1.1.ebuild:
+  Add CNS, an important package in X-ray crystallography and nuclear magnetic
+  resonance (NMR).
+
diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
new file mode 100644
index 000000000000..9ec785226809
--- /dev/null
+++ b/sci-chemistry/cns/Manifest
@@ -0,0 +1,22 @@
+AUX 1.1-time-length-10.patch 443 RMD160 664ae29ccb2921954ffb14653e4560ed2bef1fa4 SHA1 ca1ddd1535c54bd541570eaf0187eb4c6f638e13 SHA256 73ca56b80588aabd513d6f5171db1217189899e04b5e460a55824eef13c5505a
+MD5 53591c4f04cc3ac9c21ba8da86ffa24b files/1.1-time-length-10.patch 443
+RMD160 664ae29ccb2921954ffb14653e4560ed2bef1fa4 files/1.1-time-length-10.patch 443
+SHA256 73ca56b80588aabd513d6f5171db1217189899e04b5e460a55824eef13c5505a files/1.1-time-length-10.patch 443
+DIST cns_solve_1.1_basic_inputs.tar.gz 5049767 RMD160 eb5686a006d53cf269456eaecd7507842c8a10eb SHA1 255e7c5170168f9e032ef9e84a870eddf176f4ce SHA256 916d86d96159bd945a3b05e26c71af0cc6097234776385630f618fa2641cf3eb
+DIST cns_solve_1.1_data.tar.gz 18770504 RMD160 a18470f31fa6213e817dadf3c3c56231ebce9e63 SHA1 3eaae5ecd1df14412083af8a31a6e3f7b14c4753 SHA256 da59213013b845ca357decfc11337c7dfdb3134bd012c710291c66e8febdbb37
+DIST cns_solve_1.1_test.tar.gz 2852870 RMD160 2f7e7b5ed4e603b2459944a8991829d1361315b5 SHA1 c50587cf3fdfcb1266d13dbd689a9b8b094fb681 SHA256 c5d049596cca4f6985b0b4997f4fa62345d2c111b8fab534918829ade1899a23
+EBUILD cns-1.1.ebuild 3596 RMD160 467b637b41c7101441ebcf3749f41f725e793d5b SHA1 954d91d91997ef0a8cb43ba4d07129c784e9fe19 SHA256 a5bd1424acf90e99126e56fe443c92baa0fd592da9dfea25ae86bd75c724382d
+MD5 20b6eaa9cadf246a8a59cd25ce1929d6 cns-1.1.ebuild 3596
+RMD160 467b637b41c7101441ebcf3749f41f725e793d5b cns-1.1.ebuild 3596
+SHA256 a5bd1424acf90e99126e56fe443c92baa0fd592da9dfea25ae86bd75c724382d cns-1.1.ebuild 3596
+MISC ChangeLog 454 RMD160 080a1457a8206ba627138a2dabaf6336bc8c9e08 SHA1 348da519c886d9bda4524c87789e550f40199499 SHA256 1b68444dde2e600ad9977aab7914dcbbfd581ed6b7fd719665735ae55aff5efd
+MD5 47f926c4be7dc38a0d5e909551897114 ChangeLog 454
+RMD160 080a1457a8206ba627138a2dabaf6336bc8c9e08 ChangeLog 454
+SHA256 1b68444dde2e600ad9977aab7914dcbbfd581ed6b7fd719665735ae55aff5efd ChangeLog 454
+MISC metadata.xml 248 RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 SHA1 75a648fddef9922cdfe21fb0298a1c746190fd82 SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27
+MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248
+RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248
+SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248
+MD5 b385cdc2d3d0081bc11e84da22d9bdbf files/digest-cns-1.1 804
+RMD160 f61ade67504a936a20ba4da9835af097c8cae912 files/digest-cns-1.1 804
+SHA256 8d3e2c15dea9f13feb8c0f6ef3d46f5e4892a1f51175176146bd76915ff9c0cf files/digest-cns-1.1 804
diff --git a/sci-chemistry/cns/cns-1.1.ebuild b/sci-chemistry/cns/cns-1.1.ebuild
new file mode 100644
index 000000000000..7430ed6863b4
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.1.ebuild
@@ -0,0 +1,126 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.1.ebuild,v 1.1 2006/06/10 07:28:49 spyderous Exp $
+
+inherit eutils fortran toolchain-funcs
+
+MY_PN="${PN}_solve"
+MY_P="${MY_PN}_${PV}"
+
+DESCRIPTION="Crystallography and NMR System"
+HOMEPAGE="http://cns.csb.yale.edu/"
+SRC_URI="${MY_P}_basic_inputs.tar.gz
+	${MY_P}_data.tar.gz
+	test? ( ${MY_P}_test.tar.gz )"
+RESTRICT="fetch"
+LICENSE="cns"
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="test"
+RDEPEND="|| ( app-shells/tcsh app-shells/csh )
+	!app-text/dos2unix"
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+FORTRAN="g77 gfortran"
+
+pkg_nofetch() {
+	einfo "Fill out the form at http://cns.csb.yale.edu/cns_request/"
+	einfo "and place these files:"
+	einfo "${A}"
+	einfo "in ${DISTDIR}."
+}
+
+src_unpack() {
+	unpack ${A}
+
+	# The length of time must be at least 10, not 9
+	# http://gcc.gnu.org/ml/fortran/2006-02/msg00198.html
+	epatch "${FILESDIR}"/${PV}-time-length-10.patch
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	sed -i \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
+		"${S}"/cns_solve_env
+}
+
+src_compile() {
+	local GLOBALS
+	if [[ ${FORTRANC} = g77 ]]; then
+		GLOBALS="-fno-globals"
+	fi
+
+	# make install really means build, since it's expected to be used in-place
+	emake \
+		CC="$(tc-getCC)" \
+		F77="${FORTRANC}" \
+		LD="${FORTRANC}" \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		F77OPT="${FFLAGS:- -O2} \$(CNS_MALIGN_I86)" \
+		F77STD="${GLOBALS}" \
+		LDFLAGS="${LDFLAGS}" \
+		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 ..."
+	csh -c \
+		"setenv CNS_G77; source cns_solve_env; 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}:${ROOT}usr:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${ROOT}usr:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/data:g" \
+		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
+		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+		-e "s:\$CNS_LIB:\$CNS_DATA:g" \
+		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/bin/cns_info:g" \
+		"${S}"/cns_solve_env
+
+	# Get rid of setup stuff we don't need in the installed script
+	sed -i \
+		-e "83,$ d" \
+		-e "37,46 d" \
+		"${S}"/cns_solve_env
+
+	newbin "${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"
+
+	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
+
+	insinto /usr/share/cns
+	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
+	doins "${S}"/bin/cns_info
+	doins "${S}"/cns_solve_env
+
+	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/*
+}
+
+pkg_postinst() {
+	ewarn "You must source ${ROOT}usr/share/cns/cns_solve_env"
+	ewarn "before running CNS. It's a C-shell script,"
+	ewarn "so you also must be using csh or tcsh."
+}
diff --git a/sci-chemistry/cns/files/1.1-time-length-10.patch b/sci-chemistry/cns/files/1.1-time-length-10.patch
new file mode 100644
index 000000000000..2b38bad6254b
--- /dev/null
+++ b/sci-chemistry/cns/files/1.1-time-length-10.patch
@@ -0,0 +1,11 @@
+--- cns_solve_1.1.orig/instlib/machine/unsupported/g77-unix/machine_f.f	2006-06-07 11:04:45.000000000 -0700
++++ cns_solve_1.1/instlib/machine/unsupported/g77-unix/machine_f.f	2006-06-07 11:04:59.000000000 -0700
+@@ -65,7 +65,7 @@
+       CHARACTER*(*) A
+       INTEGER AMAX, ALEN
+ C local
+-      CHARACTER  DSTR*8, TSTR*9
++      CHARACTER  DSTR*8, TSTR*10
+ C begin
+       IF (AMAX.LT.8) THEN
+       WRITE(6,'(A)') ' %VTIME-ERR: string to small'
diff --git a/sci-chemistry/cns/files/digest-cns-1.1 b/sci-chemistry/cns/files/digest-cns-1.1
new file mode 100644
index 000000000000..5401e3b99cb3
--- /dev/null
+++ b/sci-chemistry/cns/files/digest-cns-1.1
@@ -0,0 +1,9 @@
+MD5 df367291cb09105eaf25ad8bdfac6dc7 cns_solve_1.1_basic_inputs.tar.gz 5049767
+RMD160 eb5686a006d53cf269456eaecd7507842c8a10eb cns_solve_1.1_basic_inputs.tar.gz 5049767
+SHA256 916d86d96159bd945a3b05e26c71af0cc6097234776385630f618fa2641cf3eb cns_solve_1.1_basic_inputs.tar.gz 5049767
+MD5 3851c61cfd4d9bdf2ff8ab752c42f717 cns_solve_1.1_data.tar.gz 18770504
+RMD160 a18470f31fa6213e817dadf3c3c56231ebce9e63 cns_solve_1.1_data.tar.gz 18770504
+SHA256 da59213013b845ca357decfc11337c7dfdb3134bd012c710291c66e8febdbb37 cns_solve_1.1_data.tar.gz 18770504
+MD5 8e6a9534f5aac30956296004d73cd14f cns_solve_1.1_test.tar.gz 2852870
+RMD160 2f7e7b5ed4e603b2459944a8991829d1361315b5 cns_solve_1.1_test.tar.gz 2852870
+SHA256 c5d049596cca4f6985b0b4997f4fa62345d2c111b8fab534918829ade1899a23 cns_solve_1.1_test.tar.gz 2852870
diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/cns/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>