Bump patches to aria-2.3.2

Package-Manager: portage-2.2.0_alpha51/cvs/Linux x86_64

5 files changed, 271 insertions, 20 deletions

diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest
index e78710569f5a..cd20eab3cda7 100644
--- a/sci-chemistry/aria/Manifest
+++ b/sci-chemistry/aria/Manifest
@@ -4,13 +4,13 @@ Hash: SHA512
 DIST aria2.3.1.tar.gz 1833973 RMD160 f2ee0bfc7e3164b5c34c81abb74256c5d76f53d7 SHA1 b257094bdaf6ba5b64645b8251d9243654e6d0fc SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc
 DIST aria2.3.2.tar.gz 1836270 RMD160 cd96f19c7a229694d561824dcca9ee22845c6a4f SHA1 74fc1cb6640b2a3f97851ac88042023f1a9c07ce SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615
 EBUILD aria-2.3.1.ebuild 2022 RMD160 e176a7b25c8d06287c91bb2c4d97f0d160dcc6d5 SHA1 28677a59f666d2ec9173ae86cfac37bc4a76f719 SHA256 0a83e234e39fbff3ffa65f21df768b7e0fea23ac13ad17008ab72e6103e3c96d
-EBUILD aria-2.3.2.ebuild 2022 RMD160 cd4b143087256e7e3f70f74f21d0638222bab866 SHA1 c3e2775845d0c1f869e5fb67cb0615585474c784 SHA256 696304d2e14b5f89924a4b14b1b015167ed6b73ae096a30b9aba38b9a7385efd
-MISC ChangeLog 1251 RMD160 56dec14841a19f9eb5a9556797f2bb1527d8d0c6 SHA1 cda64c5e01d4d6c9f8bf861dacb24dd006032bfa SHA256 a18d7bed660ba5775570608d9868bf4471754360c530e865ba9597c69056885d
+EBUILD aria-2.3.2.ebuild 2022 RMD160 f17276f2346ef63e9fbd25145f9fb26d85113018 SHA1 180e90a7f4e92d7a47d0a428bccd0155bcf002cf SHA256 738fa89aff5df458c4c61a64dd6e8ad839fdd43df50c141a34d6750f4055ebd9
+MISC ChangeLog 1381 RMD160 8b24b8bc14a46f80b17e15197c569c3c1e7fb032 SHA1 14aa7bab85559b44835b1294882629df52fd4c15 SHA256 04013a1df7bd75730ec7478d075193b6337b4f790e1416aa45fafc97c4ac034a
 MISC metadata.xml 219 RMD160 e9da2d4271f89b9dbac478d145a519318f0f3314 SHA1 6d4a101013d6a40cd61cb2d8c6b517c443013bc7 SHA256 0be94b46df4c9a73494034f33b1371769951f52890e5c857ebe1dc9bc729d0a8
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-=0oFQ
+iEYEAREKAAYFAk5c6wIACgkQgAnW8HDreRZ/TQCePvYQ83oTRwDIkb7AyiSRPt8W
+OSIAnR2qEw2O2W8+9SL5Trz0fhrKQMrl
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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/Manifest b/sci-chemistry/cns/Manifest
index 2eba8fd4b112..dd1ca16a1e39 100644
--- a/sci-chemistry/cns/Manifest
+++ b/sci-chemistry/cns/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
 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
@@ -14,6 +14,7 @@ AUX 1.3_p5-gentoo.patch 2581 RMD160 fba36e2bc6a3e4cef25ef726bc850cb1f214e44a SHA
 AUX cns_solve_env_sh 7070 RMD160 4104b22476a61a80c7adae8a363da1dd4ab4f136 SHA1 30ba978f4862fd94d9fa939cbb7c3eb55ece46cd SHA256 da571cba2a2244e571870b1783fd6cdce1b595e14234cfb43011e9e9eb50151c
 AUX cns_solve_env_sh-1.3_p5 7332 RMD160 eee19d64dc863e434159994282a78d8d576adf62 SHA1 050de938d0c0b4d1e497b03ff196416e416a0da7 SHA256 88127d99380544e502dfe3b3a7788102a7f6b30e7245b26e5e204b8b611bbc1d
 DIST aria2.3.1.tar.gz 1833973 RMD160 f2ee0bfc7e3164b5c34c81abb74256c5d76f53d7 SHA1 b257094bdaf6ba5b64645b8251d9243654e6d0fc SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc
+DIST aria2.3.2.tar.gz 1836270 RMD160 cd96f19c7a229694d561824dcca9ee22845c6a4f SHA1 74fc1cb6640b2a3f97851ac88042023f1a9c07ce SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615
 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
@@ -23,14 +24,15 @@ DIST cns_solve_1.3_all.tar.gz 61221912 RMD160 6bce0ddeb04651223be46c0d94504d57da
 EBUILD cns-1.1.ebuild 3749 RMD160 e3e939dc4bfee9acace88181d4206417d0d40099 SHA1 44bd3184af25ac3713be2914a1c3292840479d4e SHA256 18971dfaf06932193bcc31accf8a84644bb0beac67b12d1a7c4b1b89891fa2ef
 EBUILD cns-1.2.1-r5.ebuild 6843 RMD160 44c3031a036837d687989af3861dc55218ce00d7 SHA1 23c01e04d76e63831ca529694a207de33114b25e SHA256 79ad99649fcda855569f467f78ab03c9def972dd0d3b485e3ae432dd0ccd0b06
 EBUILD cns-1.2.1-r6.ebuild 6862 RMD160 025efb3adaf9b55e8d8bcab5a5b91c7aeb6cd60b SHA1 43164aecb8c6cef8ec22a3af4888e38ce063aebd SHA256 627217af33e06df4805fbe1d537fb379aad294e9564cacf59d31182c27305cb6
+EBUILD cns-1.2.1-r7.ebuild 6862 RMD160 8a8dd57c652f21fd44079a2af6774664b6bc3efb SHA1 32b6c3c207be6f14d4cbdfd9936b843147b3d104 SHA256 33b87c54cebdaa1159937c0ec0c8360c4c10a45344e803a51020d73008c013ae
 EBUILD cns-1.2.1.ebuild 5591 RMD160 f06d7b6913492eeac5e1c8cb4cdd26344a82c7b9 SHA1 37922ec85c0c872c81a65a704d9bd97659c6a2f8 SHA256 7c90b8357889c2730f40ae556608763a9e27696b5f485a8f4ed9a154d3181f8d
 EBUILD cns-1.3_p5.ebuild 6098 RMD160 1f8ae90ce32108de0acfb4f4aaa3d52c7096958a SHA1 8fb8c381acb5f5ea3584d261dea919c848ef4949 SHA256 fef533bbce218d5f3800648def3a8226c7d3611df127c338401ead0021a5c66a
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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>