Added aria support per 220905

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

9 files changed, 714 insertions, 18 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index ae3b780e7ef1..57f7d426d005 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.18 2010/02/06 12:02:19 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.19 2010/02/06 21:49:39 jlec Exp $
+
+*cns-1.2.1-r2 (06 Feb 2010)
+
+  06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/1.2.1-aria.patch, +cns-1.2.1-r2.ebuild:
+  Added aria support per 220905
+  Some QA fixes to make repoman happy
 
   06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org> cns-1.2.1-r1.ebuild:
   We have to repect selection of USE="-openmp", fixed path in setup file.
diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
index b2c7ac739a16..ed99a9f039c1 100644
--- a/sci-chemistry/cns/Manifest
+++ b/sci-chemistry/cns/Manifest
@@ -4,25 +4,28 @@ Hash: SHA1
 AUX 1.1-time-length-10.patch 443 RMD160 664ae29ccb2921954ffb14653e4560ed2bef1fa4 SHA1 ca1ddd1535c54bd541570eaf0187eb4c6f638e13 SHA256 73ca56b80588aabd513d6f5171db1217189899e04b5e460a55824eef13c5505a
 AUX 1.2-allow-unknown-architectures.patch 540 RMD160 559f16141025b3d102a316af79ba0ee195846774 SHA1 d168a0413aab5e84ea48f1de5e0a84bc7206fcc7 SHA256 47f398e4c534f01eb64a1c68d477d21a8371707a0977b900d9f2124d3d37243d
 AUX 1.2.1-allow-gcc-openmp.patch 926 RMD160 b8ccec007a717c53ca15731b1b5637bb067d2dda SHA1 b5c876271029e47e180d1dd6d51df51b648f6232 SHA256 8c650b36ef731f7b799397ac9f6abfe9cdf46508df930e7bd3a0f2a0dc2e2275
+AUX 1.2.1-aria.patch 15006 RMD160 b358747845e8d53f450e654f493dedbe400f537f SHA1 234dde547748ba95eb7b94ffac7bfcc9bfd22991 SHA256 08585a1e88b8b8da0f983e934a2859b128e4cba5e714af3b6ed40f334fdbe982
 AUX 1.2.1-gentoo.patch 2411 RMD160 a82893524541961a9797fd2bb84982e609fda717 SHA1 7d3168a9cf7622923138022a5683aa65b5d5c34d SHA256 58972606d23d87fdeb08c9e37d9d5c536983e5a1ad4647dedd5b283ef67bc52c
 AUX cns_solve_env_sh 7070 RMD160 4104b22476a61a80c7adae8a363da1dd4ab4f136 SHA1 30ba978f4862fd94d9fa939cbb7c3eb55ece46cd SHA256 da571cba2a2244e571870b1783fd6cdce1b595e14234cfb43011e9e9eb50151c
+DIST aria2.2.tar.gz 1710084 RMD160 b96a900befd5521649ccce84d4d5b93d30709799 SHA1 faa5ff9e7682026afc334f1c8b3b10259a5e69f9 SHA256 a1695ee11b06a045c4b4bb9f0113d1e48c86e12d4149c0dcb505ca894069d054
 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
 DIST cns_solve_1.21_all-mp.tar.gz 32748040 RMD160 0da9c1858e858474a8798149b7692b9e097adc9e SHA1 3ba32a6622b55dfff397b6844e8b8a594124a482 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1
 DIST cns_solve_1.21_all.tar.gz 32739912 RMD160 ab763373923264497d1ccb507cab23b2e1af9826 SHA1 93059805e14f0482cf58755daecc52cf97863215 SHA256 a581c6a0e9e5ffd45f025520959921d7ba91bb5d1e6569f1c81e709bb6f87c81
 DIST cns_solve_1.2_all.tar.gz 30456531 RMD160 45cff57b3f026d730032cfc1c9476880f7cc81ab SHA1 1611ad499746993a9d210e6053e1cdd1553848a7 SHA256 230847d8e00def4b55dda8c50d9148bca11a88ed6bc575e735041c91f8fff064
-EBUILD cns-1.1.ebuild 3605 RMD160 d909804101c942679132d7c37707e3e0f3cf3617 SHA1 b4d9f4f0fd25618e8a85d9a593c3f3e46bee2efa SHA256 81855368f4aa81e479078187e733b10625ec1a0a893c856b5d97022d64af787e
-EBUILD cns-1.2-r1.ebuild 4474 RMD160 4c00d86abde1f2c046eacbe0d0cd1a989222b724 SHA1 30284469ebd2284cebb4eaf309cc7840afe44894 SHA256 105e0688bc6ac038f97a6ed93905ed16ce15350c81ded1870892653972eb1372
+EBUILD cns-1.1.ebuild 3598 RMD160 c659528cda734552ca1faa9bc85c371b92d90d46 SHA1 e891a1be5f873e869bce5a6b617bbfd54a7aa71d SHA256 2be38322ddc333590c4d891f675921cabb0e18ef795042c1c4a849beb0793f6b
+EBUILD cns-1.2-r1.ebuild 4467 RMD160 cc3f1a26a8c28c111f25b74572dc4af3bb1d56c9 SHA1 f4da145be4190c1837e3262291f75c9eeaa3ef2d SHA256 ac40399a59987612e7602811cb79fdb4ae0295d23222afb6947ad1b79f5a8238
 EBUILD cns-1.2.1-r1.ebuild 5531 RMD160 93f382ecb94f6b6a21108182a2aae18547bc704a SHA1 f80f7203f79cd527b2ccdd2755971a21a6b87cba SHA256 0866f9e38ce28d128db71974d1832f7fc6124f0d11b02f90111cd8a5434b075c
-EBUILD cns-1.2.1.ebuild 5581 RMD160 266bdf311cc963b8f6974888890897980791655e SHA1 563c412fbc397c71b4a580e4127df56ac8c4d3e3 SHA256 686f7c10b9ca44b0d9869761467ad529994ab86e84a2808efab9e107e08cce3f
-EBUILD cns-1.2.ebuild 3504 RMD160 e3dd53a4fa0a7118f7571e7bca7819d4ad9e39b5 SHA1 926f47b6b27c48c027d903add199d5445e62b13a SHA256 9eecdffa0fbe9fa50b68ea25654aa8b48dda3abc3eec63b21a6f373cdfd2ee19
-MISC ChangeLog 3248 RMD160 3cd8b7a2c7d3b1d4d61a63a095178030dfe18d0b SHA1 2bd0f7a15900f48ef99ceebca32225effc768927 SHA256 761d19021466122ed5790c0cf9075ed3d4fd07bff440fc1bc224295126eb3782
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+EBUILD cns-1.2.1-r2.ebuild 5925 RMD160 3ec3eaf16b91ab513247c91d91ab2182f756475b SHA1 2f62e0d68a88f3cd91dff36f48665d3f26d47a34 SHA256 f4b51e823fa2fed5d2b187066bfa2848e2f209b05d0875623b8c14668daf6f33
+EBUILD cns-1.2.1.ebuild 5574 RMD160 23000fd54ce250a3dbf40ab71d12c539fda0d9fd SHA1 42c852c40d23eeec1280359d5adfe8c51a7ebf24 SHA256 7c1f6871416f516773af3cd23d8be9c2b0e978401898d5932622a2dd2b121301
+EBUILD cns-1.2.ebuild 3497 RMD160 9e097171ebd44f1a7e5dd317beeb6b65aefac2f6 SHA1 3afc4b415d2ef559b717843a05bc6afb8ee651a2 SHA256 1a6094c8bca3797e62c375a2370cc7425e9c1dd1106d20f202681bc5a87da1fc
+MISC ChangeLog 3451 RMD160 be074f842da2cffc88e2f09df8742b5cce4703c9 SHA1 070e0afc1edf77c85488802e8071bdca9356ae1a SHA256 6daf9cb8257fcc32ac0c077ba2e55c9540e2e103d9e46901caddf2743cf87eca
+MISC metadata.xml 302 RMD160 d60d9cd875115eaba68ad4b504bff76b39a136b0 SHA1 ecdd8feeea2de489927403f1941acfc582c17222 SHA256 a374144760a8ac1f72b1c625c41f98cee3f74511c964133bda119da580664c50
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-hKAAniYzYqcxRk1ajKOOv93VA6iLGjlC
-=9qMa
+iEYEARECAAYFAktt4/kACgkQgAnW8HDreRYbRACeL91+WT2Pt7YnCXHCQxQVJcQ5
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diff --git a/sci-chemistry/cns/cns-1.1.ebuild b/sci-chemistry/cns/cns-1.1.ebuild
index ea5604c97451..126e3b3eb8ff 100644
--- a/sci-chemistry/cns/cns-1.1.ebuild
+++ b/sci-chemistry/cns/cns-1.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 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 1.5 2008/06/03 02:09:01 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.1.ebuild,v 1.6 2010/02/06 21:49:39 jlec Exp $
 
 inherit eutils fortran toolchain-funcs
 
@@ -26,7 +26,7 @@ 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 ${A}
 	einfo "in ${DISTDIR}."
 }
 
diff --git a/sci-chemistry/cns/cns-1.2-r1.ebuild b/sci-chemistry/cns/cns-1.2-r1.ebuild
index c802f40bb420..dbec50254253 100644
--- a/sci-chemistry/cns/cns-1.2-r1.ebuild
+++ b/sci-chemistry/cns/cns-1.2-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2-r1.ebuild,v 1.3 2008/06/03 02:09:01 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2-r1.ebuild,v 1.4 2010/02/06 21:49:39 jlec Exp $
 
 inherit eutils fortran toolchain-funcs
 
@@ -25,7 +25,7 @@ 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 ${A}
 	einfo "in ${DISTDIR}."
 }
 
diff --git a/sci-chemistry/cns/cns-1.2.1-r2.ebuild b/sci-chemistry/cns/cns-1.2.1-r2.ebuild
new file mode 100644
index 000000000000..683f615ce923
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r2.ebuild
@@ -0,0 +1,205 @@
+# 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-r2.ebuild,v 1.1 2010/02/06 21:49:39 jlec Exp $
+
+EAPI="2"
+
+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="${MY_P}_all-mp.tar.gz
+	aria? ( aria2.2.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh
+	!app-text/dos2unix"
+DEPEND="${RDEPEND}"
+PDEPEND="aria? ( sci-chemistry/aria )"
+
+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
+
+	cd "${WORKDIR}"
+	if use aria; then
+		# Update the cns sources in aria for version 1.2.1
+		epatch "${FILESDIR}"/1.2.1-aria.patch
+
+		# Update the code with aria specific things
+		cp -rf aria2.2/cns/src/* "${S}"/source/
+	fi
+	cd "${S}"
+
+	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
+}
+
+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
+	emake \
+		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 /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=/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
+}
diff --git a/sci-chemistry/cns/cns-1.2.1.ebuild b/sci-chemistry/cns/cns-1.2.1.ebuild
index e59bb82f4dea..8595ee6447c6 100644
--- a/sci-chemistry/cns/cns-1.2.1.ebuild
+++ b/sci-chemistry/cns/cns-1.2.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2009 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.ebuild,v 1.4 2009/07/07 23:26:17 flameeyes Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1.ebuild,v 1.5 2010/02/06 21:49:39 jlec Exp $
 
 inherit eutils fortran toolchain-funcs versionator flag-o-matic
 
@@ -27,7 +27,7 @@ FORTRAN="g77 gfortran"
 pkg_nofetch() {
 	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
 	elog "and place these files:"
-	elog "${A}"
+	elog ${A}
 	elog "in ${DISTDIR}."
 }
 
diff --git a/sci-chemistry/cns/cns-1.2.ebuild b/sci-chemistry/cns/cns-1.2.ebuild
index 530cccffb32f..c33d0c0b3b85 100644
--- a/sci-chemistry/cns/cns-1.2.ebuild
+++ b/sci-chemistry/cns/cns-1.2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.ebuild,v 1.2 2008/06/03 02:09:01 mr_bones_ Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.ebuild,v 1.3 2010/02/06 21:49:39 jlec Exp $
 
 inherit eutils fortran toolchain-funcs
 
@@ -25,7 +25,7 @@ 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 ${A}
 	einfo "in ${DISTDIR}."
 }
 
diff --git a/sci-chemistry/cns/files/1.2.1-aria.patch b/sci-chemistry/cns/files/1.2.1-aria.patch
new file mode 100644
index 000000000000..35c962b882c9
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-aria.patch
@@ -0,0 +1,475 @@
+diff -arNu aria2.2/cns/src/cns.f aria2.2.new/cns/src/cns.f
+--- aria2.2/cns/src/cns.f	2007-08-22 17:25:51.000000000 +0200
++++ aria2.2.new/cns/src/cns.f	2009-06-14 15:28:39.907685273 +0200
+@@ -12,7 +12,7 @@
+ C  +          J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,          +
+ C  +          L.M.Rice, T.Simonson, G.L.Warren                     +
+ C  +===============================================================+
+-C  + Copyright 1997-2007 Yale University                           +
++C  + Copyright 1997-2008 Yale University                           +
+ C  +===============================================================+
+ C  +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ C
+@@ -470,6 +470,7 @@
+       INTEGER      HNLEN, TMP, PTRSZ, STLEN
+       CHARACTER*(1) CNSPTMP
+       CHARACTER*(4) ST
++!$    integer omp_get_max_threads
+ C
+ C write header
+       WRITE(6,'(10X,A)')
+@@ -511,7 +512,7 @@
+      &'             J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,',
+      &'             L.M.Rice, T.Simonson, G.L.Warren.'
+       WRITE(6,'(10X,A)')
+-     &' Copyright (c) 1997-2007 Yale University'
++     &' Copyright (c) 1997-2008 Yale University'
+       WRITE(6,'(10X,A)')
+      &'============================================================'
+ C
+@@ -526,6 +527,9 @@
+       WRITE(6,'(10X,7A)')
+      & ' Running on machine: ',HOSTNM(1:HNLEN),
+      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
++!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
++!$   &  ' threads'
++!$C (to change use setenv OMP_NUM_THREADS x)
+ C
+       CALL GETNAM(USERNM,12,TMP)
+       WRITE(6,'(10X,2A)')
+diff -arNu aria2.2/cns/src/energy.f aria2.2.new/cns/src/energy.f
+--- aria2.2/cns/src/energy.f	2006-12-18 16:26:49.000000000 +0100
++++ aria2.2.new/cns/src/energy.f	2009-06-14 14:47:57.421262637 +0200
+@@ -23,7 +23,8 @@
+       INTEGER I, NDIM, N
+       DOUBLE PRECISION TOTAL
+       DOUBLE COMPLEX DCVAL
+-      DOUBLE COMPLEX EDUMMY
++CCC modifcation ATB 4/27/08
++      DOUBLE PRECISION EDUMMY
+ C parameters
+       DOUBLE PRECISION ZERO, ONE
+       PARAMETER (ZERO=0.0D0, ONE=1.0D0)
+diff -arNu aria2.2/cns/src/noe.f aria2.2.new/cns/src/noe.f
+--- aria2.2/cns/src/noe.f	2007-08-22 17:25:51.000000000 +0200
++++ aria2.2.new/cns/src/noe.f	2009-06-14 15:03:30.001587922 +0200
+@@ -36,8 +36,8 @@
+       INTEGER ISLCT(*), JSLCT(*)
+ C local
+       INTEGER I, II, NISLCT, NJSLCT, ICL1, ICL2, NN, ITEMP, IEMODE
+-      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET
+-      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH
++      CHARACTER*4 CLASS, CLASS2, STEMP, SRESET, DENMODE
++      DOUBLE PRECISION SCALE, RTEMP, NOEDST, THRESH, GAMMA, KAPPA
+       LOGICAL MATCH
+ C parameter
+       DOUBLE PRECISION ZERO, ONE, SIX
+@@ -140,7 +140,7 @@
+      &     NPEAKI,HEAP(HPNPID),HEAP(HPNSPC),
+      &     HEAP(HPNPP1),HEAP(HPNPP2),HEAP(HPNHP1),HEAP(HPNHP2),
+      &     HEAP(HPNVOL),HEAP(HPCDIS),HEAP(HPCVOL),NATOM,ISLCT,NISLCT,
+-     &     JSLCT,NJSLCT,X,Y,Z)
++     &     JSLCT,NJSLCT,X,Y,Z,HEAP(HPDENINIT))
+ C===================================================================
+       ELSE IF (WD(1:4).EQ.'?   ') THEN
+       WRITE(6,'(A,I6,A,I6,A,/,A,F8.3,A,I6)')
+@@ -167,7 +167,8 @@
+ C
+ C get the class name:
+       CALL NEXTA4('class-name=',CLASS)
+-      CALL NEXTF('AVERaging=',RTEMP)
++CCC modification ATB 4/27/08
++      CALL NEXTF('AVEXponent=',RTEMP)
+       DO I=1,NOECCN
+       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
+       IF (MATCH) THEN
+@@ -179,7 +180,8 @@
+ C
+ C get the class name:
+       CALL NEXTA4('class-name=',CLASS)
+-      CALL NEXTF('AVERaging=',RTEMP)
++CCC modification ATB 4/27/08
++      CALL NEXTF('OREXponent=',RTEMP)
+       DO I=1,NOECCN
+       CALL EQSTWC(NOECNM(I),4,CLASS,4,1,1,MATCH)
+       IF (MATCH) THEN
+@@ -585,6 +587,38 @@
+       IF (NOEICV.GT.0) CALL NOEPRI(THRESH,1)
+       END IF
+ C====================================================================
++CCC modification ATB 5/02/08
++      ELSE IF (WD(1:4).EQ.'OUTD') THEN
++      CALL NOEOUT(0)
++      IF (NOEICV.GT.0) CALL NOEOUT(1)
++C====================================================================
++CCC modification ATB 4/25/08
++      ELSE IF (WD(1:3).EQ.'DEN') THEN
++      CALL NEXTWD('DEN>')
++      IF (WD(1:4).NE.'INIT'.AND.WD(1:4).NE.'UPDA') THEN
++      WRITE(6,'(A)') ' %NOE-ERR: DEN expects INIT or UPDAte'
++      ELSE
++      DENMODE=WD(1:4)
++      GAMMA=0.0D0
++      KAPPA=0.0D0
++      IF (DENMODE.EQ.'UPDA') THEN
++      CALL NEXTWD('DEN>')
++      IF (WD(1:4).NE.'GAMM') THEN
++      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects GAMMa parameter'
++      ELSE
++      CALL NEXTF('GAMMa=',GAMMA)
++      CALL NEXTWD('DEN>')
++      IF (WD(1:4).NE.'KAPP') THEN
++      WRITE(6,'(A)') ' %NOE-ERR: DEN UPDAte expects KAPPa parameter'
++      ELSE
++      CALL NEXTF('KAPPa=',KAPPA)
++      END IF
++      END IF
++      END IF 
++      CALL NOEDEN(DENMODE,GAMMA,KAPPA,0)
++      IF (NOEICV.GT.0) CALL NOEDEN(DENMODE,GAMMA,KAPPA,1)
++      END IF
++C====================================================================
+       ELSE IF (WD(1:4).EQ.'ANAL') THEN
+       CALL NEXTA4('ANALyse=',RANA)
+ C====================================================================
+@@ -683,7 +717,7 @@
+      &           NOEXCL,NPEAKI,NOEPID,NOESPC,NOEPP1,NOEPP2,NOEHP1,
+      $           NOEHP2,NOEVOL,NOECDI,
+      &           NOECVO,NATOM,ISLCT,NISLCT,
+-     &           JSLCT,NJSLCT,X,Y,Z)
++     &           JSLCT,NJSLCT,X,Y,Z,NOEDENINIT)
+ C
+ C Subroutine parses an NOE ASSIgn statement and
+ C puts the information into the NOE restraints list
+@@ -706,7 +740,7 @@
+       DOUBLE PRECISION NOEPP1(*),NOEPP2(*),NOEHP1(*),NOEHP2(*)
+       DOUBLE PRECISION NOEVOL(*), NOECDI(*),NOECVO(*)
+       INTEGER NATOM, ISLCT(*), NISLCT, JSLCT(*), NJSLCT
+-      DOUBLE PRECISION X(*), Y(*), Z(*)
++      DOUBLE PRECISION X(*), Y(*), Z(*), NOEDENINIT(*)
+ C local
+       INTEGER I, II, JJ, J, TISLCT, TJSLCT, PEAKID
+       LOGICAL SUCCES,OK
+@@ -737,6 +771,10 @@
+       CALL NEXTF('lower-average-distance=',NOELOW(NOENUM))
+       CALL NEXTF('higher-average-distance=',NOEHIG(NOENUM))
+ C
++C initialize initial DEN distance
++      NOEDENINIT(NOENUM)=ZERO
++
++C
+ C initialize time-average and running average stuff
+ C
+ C set the time-averaged distance and
+@@ -1732,6 +1770,232 @@
+       RETURN
+       END
+ C====================================================================
++      SUBROUTINE NOEOUT(ITEST)
++C
++C print a list of current NOE restraints
++C as assign statements
++C Front-end for NOEPR3
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'heap.inc'
++      INCLUDE 'noe.inc'
++      INTEGER ITEST
++C begin
++      CALL NOEPR3(ITEST,
++     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
++     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
++     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
++     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID))
++
++      RETURN
++      END
++C====================================================================
++      SUBROUTINE NOEPR3(ITEST,
++     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
++     &           NOEJLS,NOECND,NOERAV,NOERRV,
++     &           NOEDIS,NOELOW,NOEHIG,
++     &           NOEVIO,NOECV,NOEPID)
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'noe.inc'
++      INCLUDE 'mtf.inc'
++      INCLUDE 'pick.inc'
++      INCLUDE 'comand.inc'
++      INCLUDE 'numbers.inc'
++      INTEGER ITEST
++C
++C global NOE arrays on HEAP
++C restraint and atom pointers
++      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
++C classes
++      INTEGER NOECND(*)
++C averages
++      DOUBLE PRECISION NOERAV(*),NOERRV(*)
++C target distance and errors
++      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
++C number of violations
++      INTEGER NOEVIO(*)
++C time average pointer, test set, restraint number
++      INTEGER NOECV(*), NOEPID(*)
++C
++C local
++      INTEGER N, K, I, J, CLASS, NORR
++      INTEGER I1, I2
++C begin
++      IF (NOENUM.GT.0) THEN
++C
++C loop over all classes
++      DO CLASS=1,NOECCN
++      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
++     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
++     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
++      CALL WRNDIE(-5,'NOEPRI',
++     & 'DENOut not possible with POTEntial set to SYMM, HIGH, or 3DPO')
++      ELSE
++C
++C loop over all NOE's belonging to this class
++      DO N=1,NOENUM
++      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
++     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
++      IF (NOECND(N).EQ.CLASS) THEN
++C
++C     WE ONLY TAKE THE FIRST FROM EACH SET
++      NORR=NOEORR(N)+1
++C
++C     DO I=NOEIPR(NORR)+1,NOEIPR(NORR+1)
++C
++C     WE ONLY TAKE THE FIRST FROM EACH SET
++      I=NOEIPR(NORR)+1
++      K=NOEILS(I)
++      I1=K
++C
++C     WE ONLY TAKE THE FIRST FROM EACH SET
++      J=NOEJPR(NORR)+1
++      K=NOEJLS(J)
++      I2=K
++C
++      WRITE(PUNIT,'(A,I6,A,I6,A,F6.3,A,F6.3,A,F6.3)') 
++     & 'ASSIGn (id ',
++     & I1, ' ) (id ', I2, ' ) ', NOEDIS(N), 
++     & ' ', NOELOW(N), ' ', NOEHIG(N)
++C
++      END IF
++      END IF
++      END DO
++      END IF
++      END DO
++      END IF
++      RETURN
++      END
++C====================================================================
++      SUBROUTINE NOEDEN(DENMODE,GAMMA,KAPPA,ITEST)
++C
++C print a list of current NOE restraints
++C Front-end for NOEPR2
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'heap.inc'
++      INCLUDE 'noe.inc'
++      CHARACTER*4 DENMODE
++      DOUBLE PRECISION GAMMA, KAPPA
++      INTEGER ITEST
++C begin
++      CALL NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
++     &           HEAP(HPNORR),HEAP(HPNIPR),HEAP(HPNILS),HEAP(HPNJPR),
++     &           HEAP(HPNJLS),HEAP(HPNCND),HEAP(HPNRAV),HEAP(HPNRRV),
++     &           HEAP(HPNDIS),HEAP(HPNLOW),HEAP(HPNHIG),
++     &           HEAP(HPNVIO),HEAP(HPNCV), HEAP(HPNPID),
++     &           HEAP(HPDENINIT))
++
++      RETURN
++      END
++C====================================================================
++      SUBROUTINE NOEDEN2(DENMODE,GAMMA,KAPPA,ITEST,
++     &           NOEORR,NOEIPR,NOEILS,NOEJPR,
++     &           NOEJLS,NOECND,NOERAV,NOERRV,
++     &           NOEDIS,NOELOW,NOEHIG,
++     &           NOEVIO,NOECV,NOEPID,NOEDENINIT)
++      IMPLICIT NONE
++C I/O
++      INCLUDE 'cns.inc'
++      INCLUDE 'noe.inc'
++      INCLUDE 'mtf.inc'
++      INCLUDE 'pick.inc'
++      INCLUDE 'comand.inc'
++      INCLUDE 'numbers.inc'
++      CHARACTER*4 DENMODE
++      DOUBLE PRECISION GAMMA,KAPPA
++      INTEGER ITEST
++C
++C global NOE arrays on HEAP
++C restraint and atom pointers
++      INTEGER NOEORR(*),NOEIPR(*),NOEILS(*),NOEJPR(*),NOEJLS(*)
++C classes
++      INTEGER NOECND(*)
++C averages
++      DOUBLE PRECISION NOERAV(*),NOERRV(*)
++C target distance and errors
++      DOUBLE PRECISION NOEDIS(*),NOELOW(*),NOEHIG(*)
++C number of violations
++      INTEGER NOEVIO(*)
++C time average pointer, test set, restraint number
++      INTEGER NOECV(*), NOEPID(*)
++C initial den distance
++      DOUBLE PRECISION NOEDENINIT(*)
++C
++C local
++      DOUBLE PRECISION EN, NOERMS, NOERM2(NOECMX), THRESH
++      DOUBLE COMPLEX DBCOMP
++      DOUBLE PRECISION DBPREC
++      INTEGER NOENU2(NOECMX)
++      INTEGER NOEVIT
++      INTEGER N, K, I, J, CLASS, NOENUML, NORR
++      CHARACTER*6 SSAVE
++      CHARACTER*11 SSPOT
++      LOGICAL QHEAD
++C begin
++      THRESH=-0.1
++      NOERMS=ZERO
++      NOEVIT=0
++      NOENUML=0
++      IF (NOENUM.GT.0) THEN
++C
++C
++C loop over all classes
++      DO CLASS=1,NOECCN
++      NOENU2(CLASS)=0
++      NOERM2(CLASS)=ZERO
++      NOEVIO(CLASS)=0
++      IF (NOEPOT(CLASS).EQ.NOESYM.OR.
++     &    NOEPOT(CLASS).EQ.NOEHDI.OR.
++     &    NOEPOT(CLASS).EQ.NOE3DP) THEN
++      CALL WRNDIE(-5,'NOEPRI',
++     & 'DEN not possible with POTEntial set to SYMM, HIGH, or 3DPO')
++      ELSE
++C
++C loop over all NOE's belonging to this class
++      QHEAD=.TRUE.
++      DO N=1,NOENUM
++      IF ((ITEST.EQ.0.AND.NOECV(N).NE.NOEICV).OR.
++     &    (ITEST.EQ.1.AND.NOECV(N).EQ.NOEICV)) THEN
++      IF (NOECND(N).EQ.CLASS) THEN
++      NOENUML=NOENUML+1
++C
++C get NOE energy, current distance (in PCDATA(PCGEOM), and other results
++      CALL ENOE(EN,'ANAL',N)
++      NOERMS=NOERMS+PCDATA(PCDEVI)**2
++      NOERM2(CLASS)=NOERM2(CLASS)+PCDATA(PCDEVI)**2
++      NOENU2(CLASS)=NOENU2(CLASS)+1
++      IF (ABS(PCDATA(PCDEVI)).GT.THRESH) THEN
++      NOEVIO(CLASS)=NOEVIO(CLASS)+1
++      NOEVIT=NOEVIT+1
++      END IF
++C
++      IF (DENMODE.EQ.'INIT') THEN
++C
++C initialization
++      NOEDENINIT(N)=PCDATA(PCGEOM)
++CCCCxxx      NOEDIS(N)=PCDATA(PCGEOM)
++      ELSE
++C
++C update step
++      NOEDIS(N)=NOEDIS(N)+KAPPA*(GAMMA*(PCDATA(PCGEOM)-NOEDIS(N))+ 
++     &          (ONE-GAMMA)*(NOEDENINIT(N)-NOEDIS(N)) )       
++      END IF
++C
++      END IF      
++      END IF
++      END DO
++      END IF
++      END DO
++C
++      END IF
++      RETURN
++      END
++C====================================================================
+       SUBROUTINE ENOE(EN,ANALYS,NA)
+ C
+ C Routine computes force field for NOE restraints
+@@ -3357,6 +3621,7 @@
+       HPNRRV=0
+       HPNNSP=0
+       HPNDIS=0
++      HPDENINIT=0
+       HPNLOW=0
+       HPNHIG=0
+       HPNWGH=0
+@@ -3373,7 +3638,6 @@
+       HPNVOL=0
+       HPCVOL=0
+       HPCDIS=0
+-      HPNPRD=0
+ C
+ C
+ C reset other variables
+@@ -3463,6 +3727,7 @@
+       IF (HPNRRV.NE.0) CALL FREHP(HPNRRV,IREAL8(NOEMAX))
+       IF (HPNNSP.NE.0) CALL FREHP(HPNNSP,INTEG4(NOEMAX))
+       IF (HPNDIS.NE.0) CALL FREHP(HPNDIS,IREAL8(NOEMAX))
++      IF (HPDENINIT.NE.0) CALL FREHP(HPDENINIT,IREAL8(NOEMAX))
+       IF (HPNLOW.NE.0) CALL FREHP(HPNLOW,IREAL8(NOEMAX))
+       IF (HPNHIG.NE.0) CALL FREHP(HPNHIG,IREAL8(NOEMAX))
+       IF (HPNWGH.NE.0) CALL FREHP(HPNWGH,IREAL8(NOEMAX))
+@@ -3495,6 +3760,7 @@
+       HPNRRV=0
+       HPNNSP=0
+       HPNDIS=0
++      HPDENINIT=0
+       HPNLOW=0
+       HPNHIG=0
+       HPNWGH=0
+@@ -3511,7 +3777,6 @@
+       HPNVOL=0
+       HPCVOL=0
+       HPCDIS=0
+-      HPNPRD=0
+ C
+ C now allocate new space
+       IF (NOENEW.GT.0) THEN
+@@ -3536,6 +3801,7 @@
+       HPNRRV=ALLHP(IREAL8(NOENEW))
+       HPNNSP=ALLHP(INTEG4(NOENEW))
+       HPNDIS=ALLHP(IREAL8(NOENEW))
++      HPDENINIT=ALLHP(IREAL8(NOENEW))
+       HPNCND=ALLHP(INTEG4(NOENEW))
+       HPNJLS=ALLHP(INTEG4(NOENEW))
+       HPNJPR=ALLHP(INTEG4(NOENEW))
+diff -arNu aria2.2/cns/src/noe.inc aria2.2.new/cns/src/noe.inc
+--- aria2.2/cns/src/noe.inc	2007-08-22 17:25:51.000000000 +0200
++++ aria2.2.new/cns/src/noe.inc	2009-06-14 15:24:50.995208687 +0200
+@@ -29,6 +29,9 @@
+ C list for distances and +/- error estimates (heap pointers)
+       INTEGER HPNDIS, HPNLOW, HPNHIG
+ C
++C list for initial DEN distances
++      INTEGER HPDENINIT
++C
+ C individual weights on restraints
+       INTEGER HPNWGH
+ C
+@@ -119,7 +122,7 @@
+       INTEGER HPNVIO, HPNEXC, HPNNUM
+ 
+ C peak identifier
+-      INTEGER NPEAKI, HPNPID, HPNPRD
++      INTEGER NPEAKI, HPNPID
+ C
+ C
+ C
+@@ -142,7 +145,7 @@
+      &              NMONO,  RAVEXP, NOECOR, NOEICV, 
+      &              HPNVIO, HPNEXC, HPNNUM,
+      &              NPEAKI, HPNPID, IDIMER, HPNPP1, HPNPP2, 
+-     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPNPRD
++     &              HPNHP1, HPNHP2, HPNVOL, HPCVOL, HPCDIS, HPDENINIT
+ C
+ C     character string block
+ C
diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml
index 9ac9ffdb3a41..9d53ac3f3a11 100644
--- a/sci-chemistry/cns/metadata.xml
+++ b/sci-chemistry/cns/metadata.xml
@@ -2,4 +2,10 @@
 <!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>
 </pkgmetadata>