(#121066) Port to modular X. Add some die messages to -r2 so the die's aren't completely unhelpful. Fix the path expansion for html docs so it doesn't break the installation -- not sure how it got committed as is: {*.html *.gif} is missing a comma.

Package-Manager: portage-2.1_pre4-r1

5 files changed, 70 insertions, 41 deletions

diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
index 0339ff04af1a..a7865485fe44 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,4 +1,12 @@
-MD5 ab525fd01e6f22fee5fec0c376f35be2 ChangeLog 2089
-MD5 a72da78ea67f9b3bc3f70a62d7289660 clustalx-1.83-r2.ebuild 1820
+MD5 ac653f038113e36f51ee40e77b88393b ChangeLog 2199
+RMD160 9e52c4d5055e6dec47684a5dce7bba29ed670b3c ChangeLog 2199
+SHA256 7f99d88df2ea1a3ec48e1baf341e3a874bfba1699c0fba6aa01ce8d36034830a ChangeLog 2199
+MD5 432fb97fddf4a98d7af719d88af5ee97 clustalx-1.83-r2.ebuild 1811
+RMD160 4e0b8cc235ee97970db188feaf7482c0f6754234 clustalx-1.83-r2.ebuild 1811
+SHA256 01e47f0d0f8790b9960f356d66552d0db0f7347cbdb2ccb0b8af887736cb2172 clustalx-1.83-r2.ebuild 1811
 MD5 800c4da737d4fb9af3d8ffb7f6f44892 files/digest-clustalx-1.83-r2 68
+RMD160 65c6bfb6865cb3a790c0466dd594284b8976747b files/digest-clustalx-1.83-r2 68
+SHA256 e64e9220cac76c247d185b90b3d417d4e6aeaeb83d717f02c8a7bbc43e969e8d files/digest-clustalx-1.83-r2 68
 MD5 272b5b012593acd07a7a60b8b64e6761 metadata.xml 509
+RMD160 8155edab5beffeda8d6df320573352ea504a89bf metadata.xml 509
+SHA256 93b284c12f6e617dfd733e267fe79d561336958c4ad9b9e5c3dfb88eb01f6583 metadata.xml 509
diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 6f516752bdac..f3446d09456c 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.37 2006/01/21 18:03:06 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.38 2006/02/01 09:10:15 spyderous Exp $
+
+  01 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>;
+  ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild:
+  (#121066) Port to modular X. Add some die messages to -r2 so the die's
+  aren't completely unhelpful. Fix the path expansion for html docs so it
+  doesn't break the installation -- not sure how it got committed as is:
+  {*.html *.gif} is missing a comma.
 
   21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
   -ncbi-tools-20050605-r1.ebuild:
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 2ffd558cad43..25218af080af 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,9 +1,27 @@
-MD5 8d2365293a75e6657b3a48dc0f4570f4 ChangeLog 9019
+MD5 20cc47f212861260c8c8a9f6c2406c5f ChangeLog 9394
+RMD160 e0ec7f976d99aae31415afbb3b07ad9f25a80e70 ChangeLog 9394
+SHA256 aca6ceda82b96db48131a3b84720d147651f823476e6922ab120e29f4d5655e3 ChangeLog 9394
 MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
+RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b files/21ncbi-r1 232
+SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411 files/21ncbi-r1 232
 MD5 9cef4ca17113d005c44d3bf3d330f747 files/digest-ncbi-tools-20050605 144
+RMD160 f2ec6aacb5969800126c308f95e09b493112739b files/digest-ncbi-tools-20050605 144
+SHA256 ca6daabc7c7f08d62f06d03cc5eeb3e1fedf3bd5429cc8a16fc31ceb56744439 files/digest-ncbi-tools-20050605 144
 MD5 2f82cbf863fc3fc2522b55f74f9c3244 files/digest-ncbi-tools-20050605-r2 207
+RMD160 59b765ffd2d8d8f6a1ba2a2e2ba2568d951e0d25 files/digest-ncbi-tools-20050605-r2 207
+SHA256 eef6f31032af69e1bf8eb4f58b57d0b8679b3870158daab07dc98b0fb8e49dbd files/digest-ncbi-tools-20050605-r2 207
 MD5 6b62beda180ee6d7d4d4a52507acc3ff files/ncbi-tools-20050605-lop.patch 701
+RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 files/ncbi-tools-20050605-lop.patch 701
+SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc files/ncbi-tools-20050605-lop.patch 701
 MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
+RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 files/ncbirc 33
+SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e files/ncbirc 33
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
-MD5 9315c657c5b2919039e9f8cfb69efa75 ncbi-tools-20050605-r2.ebuild 6426
-MD5 27f1ef207c35088c37ca584b6158bd03 ncbi-tools-20050605.ebuild 5688
+RMD160 f02847af149737bf8044b3de239c5bd4b42abca5 metadata.xml 254
+SHA256 3392ded43ad861595a8cfeb0441342fdbcd6e731b4793c3e8a22ff927ce09f27 metadata.xml 254
+MD5 79c626c421b1ad1a9b5231e5eae2e94d ncbi-tools-20050605-r2.ebuild 6614
+RMD160 f0920023045cbe9f694e89b3f84d3acea911ca02 ncbi-tools-20050605-r2.ebuild 6614
+SHA256 d06902e7867e1ff217af64f03023ecb2ba3081d3820591471ec67077bdab1a28 ncbi-tools-20050605-r2.ebuild 6614
+MD5 c3c0d582d093e9a1b2df2788859a647c ncbi-tools-20050605.ebuild 5677
+RMD160 e3a90edec7d05b46b213885d67182f3b067f9877 ncbi-tools-20050605.ebuild 5677
+SHA256 d35149417de2deb43789a8342667c5a10ccd950c23b051c7d202ce9bc4ff289a ncbi-tools-20050605.ebuild 5677
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
index 48724ff87ce3..3c0ef831d1b3 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild,v 1.1 2005/12/14 20:24:03 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild,v 1.2 2006/02/01 09:10:15 spyderous Exp $
 
 inherit flag-o-matic toolchain-funcs eutils
 
@@ -19,9 +19,7 @@ DEPEND="app-shells/tcsh
 	dev-lang/perl
 	media-libs/libpng
 	mpi? ( virtual/mpi )
-	X? ( virtual/x11
-		virtual/motif
-	)"
+	X? ( virtual/motif )"
 
 S="${WORKDIR}/ncbi"
 
@@ -122,14 +120,14 @@ src_compile() {
 }
 
 src_install() {
-	dobin "${S}"/bin/* || die
-	dolib "${S}"/lib/* || die
+	dobin "${S}"/bin/* || die "dobin"
+	dolib "${S}"/lib/* || die "dolib"
 	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || die
+	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || die "includes"
 
 	if use mpi; then
 		cd "${WORKDIR}"/mpiblast-1.4.0
-		make install DESTDIR="${D}" || die
+		make install DESTDIR="${D}" || die "mpiblast"
 	fi
 
 	# TODO: Web apps
@@ -140,28 +138,28 @@ src_install() {
 	# TODO: Add support for wwwblast.
 
 	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || die
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || die
-	newdoc "${S}"/config/README README.config || die
-	newdoc "${S}"/network/encrypt/README README.encrypt || die
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || die
-	newdoc "${S}"/sequin/README README.sequin || die
-	doman "${S}"/doc/man/* || die
+	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || die "docs"
+	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || die "docs"
+	newdoc "${S}"/config/README README.config || die "docs"
+	newdoc "${S}"/network/encrypt/README README.encrypt || die "docs"
+	newdoc "${S}"/network/nsclilib/readme README.nsclilib || die "docs"
+	newdoc "${S}"/sequin/README README.sequin || die "docs"
+	doman "${S}"/doc/man/* || die "docs"
 
 	# Hypertext user documentation
-	dohtml "${S}"/{README.html,doc/{*.html *.gif}} || die
-	insinto /usr/share/doc/${PF}/html/blast || die
-	doins "${S}"/doc/blast/* || die
+	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || die "dohtml"
+	insinto /usr/share/doc/${PF}/html/blast || die "insinto html"
+	doins "${S}"/doc/blast/* || die "doins html"
 
 	# Developer documentation
 	if use doc; then
 		# "socks" documentation
 		SOCKS="network/socks/socks.cstc.4.2"
 		insinto /usr/share/doc/${PF}/socks
-		doins "${S}"/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects} || die
+		doins "${S}"/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects} || die "doins"
 		newins "${S}"/${SOCKS}/libident/README README.libident
-		doins "${S}"/${SOCKS}/sockd/sockd.conf.sample || die
-		doman "${S}"/${SOCKS}/{doc/*.{1,5,8},libident/ident.3} || die
+		doins "${S}"/${SOCKS}/sockd/sockd.conf.sample || die "doins"
+		doman "${S}"/${SOCKS}/{doc/*.{1,5,8},libident/ident.3} || die "doman"
 
 		# "regexp" documentation (No longer installed, see bug #115463.)
 		# insinto /usr/share/doc/${PF}/regexp
@@ -172,24 +170,24 @@ src_install() {
 
 		# Hypertext SDK documentation
 		insinto /usr/share/doc/${PF}/html/sdk
-		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
+		doins "${WORKDIR}"/${PN}-sdk-doc/* || die "doins"
 
 		# Demo programs
 		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
-		mv "${S}"/regexp/demo "${D}"/usr/share/ncbi/demo/regexp || die
-		mv "${S}"/regexp/test "${D}"/usr/share/ncbi/demo/regexp/test || die
+		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die "mv"
+		mv "${S}"/regexp/demo "${D}"/usr/share/ncbi/demo/regexp || die "mv"
+		mv "${S}"/regexp/test "${D}"/usr/share/ncbi/demo/regexp/test || die "mv"
 	fi
 
 	# Shared data (similarity matrices and such) and database directory.
 	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die
-	dodir /usr/share/ncbi/formatdb || die
+	doins "${S}"/data/* || die "doins"
+	dodir /usr/share/ncbi/formatdb || die "doins"
 
 	# Default config file to set the path for shared data.
 	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die
+	newins "${FILESDIR}"/ncbirc .ncbirc || die "doins"
 
 	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die
+	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "doins"
 }
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
index f5477f492ef7..2dffbf36a223 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.10 2005/11/09 05:03:53 weeve Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.11 2006/02/01 09:10:15 spyderous Exp $
 
 inherit flag-o-matic toolchain-funcs eutils
 
@@ -17,9 +17,7 @@ IUSE="doc X"
 DEPEND="app-shells/tcsh
 	dev-lang/perl
 	media-libs/libpng
-	X? ( virtual/x11
-		virtual/motif
-	)"
+	X? ( virtual/motif )"
 
 S="${WORKDIR}/ncbi"