Pruned old version

(Portage version: 2.1.1-r1)
 (Unsigned Manifest commit)

3 files changed, 4 insertions, 223 deletions

diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 4e2502922381..bef6e2eef9c9 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -14,16 +14,11 @@ AUX ncbirc 33 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 SHA1 eb14976d464f4
 MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 files/ncbirc 33
 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e files/ncbirc 33
-DIST mpiBLAST-1.4.0.tgz 344877 RMD160 ec7e7ed6be2334b1c731234c65bdd8757b770031 SHA1 f01f866a5e2161dcc3f2299f4c72b9878fef1a7e SHA256 e95a4c88642790399a888f10c240733b9cf281398f931172ff8fbc56b0706cee
 DIST mpiblast-20060625.tar.gz 165096 RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 SHA1 e0acdde2770973b752396a6ba1a99b47ea4ddcde SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097
 DIST ncbi-tools-20050605.tar.gz 14458684 RMD160 82d3c008e9b1741e8ac286d66c1ad68693663590 SHA1 7e1ddd3f049df7c906f2681453c5e5a7b12622d8 SHA256 e0108faeb84da35da82acaa925c084fbeb455c5e571cdcaae5b02c612df46209
 DIST ncbi-tools-20060507.tar.gz 15396356 RMD160 56114d25ace0338d1ef5c8c2a3cc36ce740a12e3 SHA1 64269236b09fba29d4afe0cd8a3ac6a47fee5218 SHA256 b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129
 DIST ncbi-tools-20061015.tar.gz 15772715 RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 SHA1 4e7990e9fed1cc507d10a1b5285e51dc183d318a SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
-EBUILD ncbi-tools-20050605-r2.ebuild 7006 RMD160 6b4b34d6fb3e5c83f83f96cbdf501cf9caf52fd7 SHA1 f704742dfb43e554874c1b5691910072f8e944ec SHA256 2607ff37cf893e92359987972384e099e7152294c65c93cd6a6da9334aae689f
-MD5 3d7210703a9b44f5b7bb11298eb4848a ncbi-tools-20050605-r2.ebuild 7006
-RMD160 6b4b34d6fb3e5c83f83f96cbdf501cf9caf52fd7 ncbi-tools-20050605-r2.ebuild 7006
-SHA256 2607ff37cf893e92359987972384e099e7152294c65c93cd6a6da9334aae689f ncbi-tools-20050605-r2.ebuild 7006
 EBUILD ncbi-tools-20050605.ebuild 5666 RMD160 8651f586fe414b3b67895467d8b3a89bdcb870d4 SHA1 7732a5d0c3f08a539003877926e2097e9af65320 SHA256 d4a5715743028681d3b3853fdba7e5d9e985cc18c2a198a02e9ebc2cab1e5a75
 MD5 c1ff0f85fcc84dc70c77f129684e5911 ncbi-tools-20050605.ebuild 5666
 RMD160 8651f586fe414b3b67895467d8b3a89bdcb870d4 ncbi-tools-20050605.ebuild 5666
@@ -36,10 +31,10 @@ EBUILD ncbi-tools-20061015.ebuild 6412 RMD160 315191efc3ae1cbe17069cda2a6e759734
 MD5 4d1e3aa7575d583fba120b108d351504 ncbi-tools-20061015.ebuild 6412
 RMD160 315191efc3ae1cbe17069cda2a6e759734ac800b ncbi-tools-20061015.ebuild 6412
 SHA256 d12c8cb1f1b04455c375b4e1416b55af676a35274bbe9028251150964a0bb80c ncbi-tools-20061015.ebuild 6412
-MISC ChangeLog 11279 RMD160 8b3db57249684b6eec998a9a80e5f69ec237a7ef SHA1 112ed20b5866a684fd224fa43dc2328ddcde739d SHA256 f42af77a37cf9d478737a97f4a539e348e711a0cee8d6c615f3f11d548f4dbeb
-MD5 9f1d3ff16f6c7de8390949d0a73b35c5 ChangeLog 11279
-RMD160 8b3db57249684b6eec998a9a80e5f69ec237a7ef ChangeLog 11279
-SHA256 f42af77a37cf9d478737a97f4a539e348e711a0cee8d6c615f3f11d548f4dbeb ChangeLog 11279
+MISC ChangeLog 11389 RMD160 694d9fc2d9425cd4432bba07ac4d653bd2d8bc47 SHA1 ae52fb5ecbdd96988f3e4c77766ac5aafeb894ab SHA256 583bfbf4f680bfd52b656ad775bd9610dc4b357e9611af62fc70cd6a3177b765
+MD5 3c3b85d9b57b46cfad1b38adfe441857 ChangeLog 11389
+RMD160 694d9fc2d9425cd4432bba07ac4d653bd2d8bc47 ChangeLog 11389
+SHA256 583bfbf4f680bfd52b656ad775bd9610dc4b357e9611af62fc70cd6a3177b765 ChangeLog 11389
 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
 MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
@@ -47,9 +42,6 @@ SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata
 MD5 b1b126e6be171d8c955e20e09d38ef31 files/digest-ncbi-tools-20050605 524
 RMD160 bc4d3664b8227f3749cebeb04e87df32cf574b41 files/digest-ncbi-tools-20050605 524
 SHA256 8b4847f987b8741efff3b3db0b1d2856f15c53291362ab0bfba1af21263de19c files/digest-ncbi-tools-20050605 524
-MD5 fcd61f0948a43b902b08ce382eb2a1e1 files/digest-ncbi-tools-20050605-r2 759
-RMD160 563f61cf4231e327e4aef7530d14a6c301e43d7a files/digest-ncbi-tools-20050605-r2 759
-SHA256 3accc0c62ee18b7ad56d3d6005fb33add90a80503e22c53792cf7a9686b92c21 files/digest-ncbi-tools-20050605-r2 759
 MD5 96f59d6f4dcd072b2744878ce377b23d files/digest-ncbi-tools-20060507 777
 RMD160 d0a656e48f738e1a30061121a7fecf6e5b7ee841 files/digest-ncbi-tools-20060507 777
 SHA256 d20530e140a48cab2fc12df5a0bf0957e956a6ea35a07b5b5ed42a43466ad4d7 files/digest-ncbi-tools-20060507 777
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
deleted file mode 100644
index 7939df48961e..000000000000
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
+++ /dev/null
@@ -1,9 +0,0 @@
-MD5 76a5f1b547b40dcb00ae3790579dba1b mpiBLAST-1.4.0.tgz 344877
-RMD160 ec7e7ed6be2334b1c731234c65bdd8757b770031 mpiBLAST-1.4.0.tgz 344877
-SHA256 e95a4c88642790399a888f10c240733b9cf281398f931172ff8fbc56b0706cee mpiBLAST-1.4.0.tgz 344877
-MD5 61864b4999390eb69e60734b3b02c149 ncbi-tools-20050605.tar.gz 14458684
-RMD160 82d3c008e9b1741e8ac286d66c1ad68693663590 ncbi-tools-20050605.tar.gz 14458684
-SHA256 e0108faeb84da35da82acaa925c084fbeb455c5e571cdcaae5b02c612df46209 ncbi-tools-20050605.tar.gz 14458684
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
-RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568
-SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
deleted file mode 100644
index 2acb90a89cb7..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
+++ /dev/null
@@ -1,202 +0,0 @@
-# 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 1.5 2006/10/25 19:46:02 grobian Exp $
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications (BLAST, entrez, ddv, udv, sequin...) for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="mirror://gentoo/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )
-	mpi? ( mirror://gentoo/mpiBLAST-1.4.0.tgz )"
-
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
-IUSE="doc mpi X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	mpi? ( virtual/mpi )
-	X? ( virtual/motif )"
-
-S="${WORKDIR}/ncbi"
-
-pkg_setup() {
-	echo
-	ewarn 'It is important to note that the NCBI tools (especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled. If you experience difficulties with this'
-	ewarn 'package and use agressive "CFLAGS", lower the "CFLAGS" and try'
-	ewarn 'to install the NCBI tools again.'
-	echo
-}
-
-src_unpack() {
-	unpack ${A}
-
-	if use ppc64; then
-		cd "${S}"
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if use mpi; then
-		cd "${S}"
-		epatch "${WORKDIR}"/mpiblast-1.4.0/ncbi_Jun2005_evalue.patch
-	fi
-
-	if ! use X; then
-		cd "${S}"/make
-		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-			-i makedis.csh || die
-	else
-		if use x86; then
-			# X applications segfault on startup on x86 with -O3.
-			replace-flags '-O3' '-O2'
-		fi
-	fi
-
-	# Apply user C flags...
-	cd "${S}"/platform
-	# ... on x86...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
-		-i linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux.ncbi.mk || die
-
-	# Put in our MAKEOPTS (doesn't work).
-	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
-
-	# Set C compiler...
-	# ... on x86...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
-	# ... on alpha...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
-	# ... on hppa...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
-	# ... on ppc...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-}
-
-src_compile() {
-	cd "${WORKDIR}"
-	ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast-1.4.0
-		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
-		emake || die
-	fi
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast-1.4.0
-		make install DESTDIR="${D}" || die "Failed to install MPI blast."
-	fi
-
-	# TODO: Web apps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-	# TODO: Add support for wwwblast.
-
-	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
-		die "Failed to install basic documentation."
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
-		die "Failed renaming fa2htgs documentation."
-	newdoc "${S}"/config/README README.config || \
-		die "Failed renaming config documentation."
-	newdoc "${S}"/network/encrypt/README README.encrypt || \
-		die "Failed renaming encrypt documentation."
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
-	die "Failed renaming nsclilib documentation."
-	newdoc "${S}"/sequin/README README.sequin || \
-		die "Failed renaming sequin documentation."
-	doman "${S}"/doc/man/* || \
-		die "Failed to install man pages."
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
-		die "Failed to install HTML documentation."
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# "socks" documentation
-		SOCKS="network/socks/socks.cstc.4.2"
-		insinto /usr/share/doc/${PF}/socks
-		doins "${S}"/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects} || die
-		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
-
-		# "regexp" documentation (No longer installed, see bug #115463.)
-		# insinto /usr/share/doc/${PF}/regexp
-		# doins "${S}"/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt}
-		# insinto /usr/share/doc/${PF}/regexp/html
-		# doins "${S}"/regexp/doc/*.html
-		# doman "${S}"/regexp/doc/*.{1,3}
-
-		# Hypertext SDK documentation
-		insinto /usr/share/doc/${PF}/html/sdk
-		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
-
-		# 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 "${D}"/usr/share/ncbi/demo/regexp/test || die
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/* || die "Failed to install shared data."
-	dodir /usr/share/ncbi/formatdb || die
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}