Version Bump

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 200 insertions, 5 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 0228cde06978..b34e5b283c9e 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.163 2015/03/05 20:44:57 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.164 2015/03/11 15:23:47 jlec Exp $
+
+*ccpn-2.4.2 (11 Mar 2015)
+
+  11 Mar 2015; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.2.ebuild,
+  ccpn-2.4.1_p150226.ebuild:
+  Version Bump
 
   05 Mar 2015; Justin Lecher <jlec@gentoo.org> -ccpn-2.4.1.ebuild,
   -ccpn-2.4.1_p150108.ebuild, -ccpn-2.4.1_p150122.ebuild,
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index a158ad9c199c..f12c4d71570b 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX 2.3.1-parallel.patch 850 SHA256 38f796a18c75b2ffb1168d22d1e1453faa480e4c8b0e3d75db2b0603ac4d6788 SHA512 0597e21c03baa27e2342249814fc0700b73cf2800173468574ef704d48f7e6e042ac6ae552bbb9e27fd4baca36cfaf60a1eac9813354916b3e8295a35b64dcdf WHIRLPOOL 7fec03d065add264de91aa07c211003e2471e77035f36c497c325c4319e999d83c06ef6f496ebab966d0877c89101e26ec7ce86ea8b740973c0254ad118e3e26
 AUX analysis 283 SHA256 f348aa9c9a5f7f380836b0dc62d8a1c053f69e60a441c7ae4abc45f9d8374a7b SHA512 f2dd8216021201b0f9307f8bb82033c3ebb1c9f21450ae206e59ad6442b0cf0f8fc6e4817d4347eb78a9528ba1ef60bd5395708067352d11330215e5ce2568ff WHIRLPOOL 52b60235b6a0421c985d06e28622b88106f9f24395dd9598e83d956f3c619d67248f7c71ac8c211167e06f0540a8aed16c2ce1f8369730c6fbb62269f7384fcd
 AUX dangle 279 SHA256 650da642809c8e65d7bed46465b557b4388c9b04556d860d8fbb07e35c960b7b SHA512 21fca09578aa13819a20f08ff414ca2b8d08d177a1ab09f8d85c53ae20fc6f38ab46e2933d72c239029b37ec5eebc3162f0c8e99f1ca1dd20aaa49277fac4e7d WHIRLPOOL f9b768f524a1c25e340e5738aef293140c39e49c8f287788fd8f6a2d921c9d72f3ab4333493cc4428d71b4942864801e23e46e1e72976c50e1325e58a257f9df
@@ -10,7 +13,28 @@ AUX pipe2azara 290 SHA256 d656e61005b0a5e49fdf835febac8ad334fa946fadf577072ed699
 AUX talosn.patch 1358 SHA256 55e4e412158b851f040ac25d93b8b1a42ffa6354c26327cb8803288621787518 SHA512 fb4b74d0b07b9edf47135bb5d965b485ee62fde8e33c3b4dffb09092063368de6ae54435fc82aca87d88dd9a71cb1abb96446241c7d433bd2b0b1801e3e5ed5b WHIRLPOOL 5ff7c76822d8de0545d235118d50b80c0c6321d6b11ce9f3f0d1f36ae0c68d9d5753fdc8f81ef95b46345085c5dd6a349fdc70ff7f22a7e195fcf26d4475211c
 AUX xeasy2azara 288 SHA256 e116e19f3cb7bb10a75b75608ae6efb93dfb710e86fece357f3003913673f14a SHA512 e9a3dedc155f9f7b163eead73099532653454a7f5f12042348abf87a4e8930cb8b0b66fd87ef9fcc3b395c92d7e4942829ec8f5e7a1c28c7b3ce51022b8fce6b WHIRLPOOL e021756a059dfdf0f7dfdbac0f1740ec90a31d1b0f2b70d588d7574a0fe4f0607ecfc52b58a7e3f5140ff4e7fc4054f8fa11fa467aa41a2ad09ac99a24678979
 DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d728907b251fe337758ba5bef106 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 WHIRLPOOL b53fc0438a878a8f8ce0244f5c1ce9edb616665149a699364e3bcd38c5db548c22b80ef67b4183ad5321b71b69a3b85aecc7d912893bba947700003a411651ac
+DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c2ace8ece9194be00c1fe4b2903 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b WHIRLPOOL 4499dcb074d445bfc972f9dea43e6f3e3c28722d513dce0fec4e1b2b5dab8be098f53f82565d86a4e7935f0595ef303465668230aa61021cf88e13cce8606214
 DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1
-EBUILD ccpn-2.4.1_p150226.ebuild 4665 SHA256 44cdb0520b2b85dc73cbdfc88f44a295248ac0e45cbdbb26903926ed402d6286 SHA512 10e2803cac416d7b0c72cb7eb00ca7feb6288b58a60b0380f6af10245fa50ca0f7ba73ce0217f5436e6f5a8d68e9e8b7f21eadb9090a25186b308bfc8f5a3b4c WHIRLPOOL 05c39ea06d48ef3e2d7dfcf1c494b4c96cd237c611b4df41bff0afa782af949d387aa63f0820f7f48186ad5243bde730b336d3658a17cb5622d67bba107c9d19
-MISC ChangeLog 30963 SHA256 387b6e215328a7c4b899a988d1d50ff6d3652bc2e70a3447bfa7fe7ae806a2cd SHA512 796aa95922f97a8f067ff5a96df49c2787ab15f4c5cf19426e703f9d709e0d94e7d75a19f9203fa9772f849ea4c72005498e1ab93b12e9ea46b17d4c866f979a WHIRLPOOL f5a9a368095e0fccb02759a558ee46963155644511e9fcfaaedf5404e738ecbc49839c820eef123168015932b00b06787a75596899252c7f3d4c48a4a1de8fcb
+EBUILD ccpn-2.4.1_p150226.ebuild 4663 SHA256 6c1dabe2bc98de950634a6d70539ed1fb459e6197e1745f93254ad5cf0652d12 SHA512 43d771890afced54c29c2a30118a622125f9c47e137e1662b9f3ce048498a137dd495d61844ea1514868b94767538c0f368c2f00da6e72709429943267ee03d1 WHIRLPOOL 7f81b441dae290999ee4e50f0f9e95dc20835f35b658ebd76b316441d250dbcb8ab209b1b85ff2f310205c1425bd25c7ad4496b9e19efbdc70b622f407b05be4
+EBUILD ccpn-2.4.2.ebuild 4656 SHA256 08661857f887ef9da418d500dafbba34c7a80910d19a17f287f7f9607ec0a860 SHA512 bd862d9e20b320aca7c28261cd16071c300fa94f36bec2f6640e39b5a985f642257cb3513c198fc9ebf1c994f14c57ba3b93f385364698e5f1f26db3b90e8c59 WHIRLPOOL 3b87bc53a3fb2bf88d602dc5684f3de7cf3616896d814cb793132aefd4d78bf2830c057dea0b4644edc5488dcb3781d9223fb0e2603d5c03ba3c8b264d01cf52
+MISC ChangeLog 31102 SHA256 1425aadbe7b89d0548accb5fe662d87d8a23e3bdb44b41de89f045dcd24bd035 SHA512 93e0859fc144af9fb90744f131a4d87f7c06a3ad1dc4eab3454c66a8d7b2975fcc396ed1ffe1c21c4be823b73da1551d43d826cff54e2e9062c1f8329dbabe96 WHIRLPOOL 8ee3bc52c06b8457fb72b1f3c2e1d481df55cb4bec430144d1633b985d8bf0e4a5c1ed1a11d26c3c3cbb203b89c8d7434f2a5159409dbecc191918aad43a301f
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
index f9b540e85161..1333b404c9e1 100644
--- a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild,v 1.1 2015/02/26 07:50:22 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild,v 1.2 2015/03/11 15:23:47 jlec Exp $
 
 EAPI=5
 
@@ -126,7 +126,7 @@ src_install() {
 	for wrapper in ${_wrapper}; do
 		sed \
 			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
-		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
 			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
 			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
 			-e "s|gentoopython|${EPYTHON}|g" \
diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
new file mode 100644
index 000000000000..c7092b446957
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.2.ebuild,v 1.1 2015/03/11 15:23:47 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="ssl,tk"
+
+inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
+
+#PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+[[ -n ${PATCHSET} ]] \
+	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/tk[threads]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/2.3.1-parallel.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_TRUE"
+		GL_DIR="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS=""
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	rm -rf data model doc license || die
+
+	sed \
+		-e "s|/usr|${EPREFIX}/usr|g" \
+		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
+		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
+		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
+		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
+		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
+		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
+		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
+		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
+		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
+		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
+		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
+		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete || die
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
+			-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|${EPYTHON}|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper}
+	done
+
+	local in_path=$(python_get_sitedir)/${PN}
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+	sed \
+		-e 's|#from __future__|from __future__|g' \
+		-i ${i} || die
+	done
+
+	dodir ${in_path#${EPREFIX}}/c
+
+	ebegin "Installing main files"
+		python_moduleinto ${PN}
+		python_domodule python
+	eend
+
+	ebegin "Adjusting permissions"
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+	python_optimize
+}