Removed buggy version

Package-Manager: portage-2.0.53

4 files changed, 13 insertions, 206 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 79351828b3c0..6f516752bdac 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/ncbi-tools
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.36 2005/12/14 20:24:03 ribosome Exp $
+# 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 $
+
+  21 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+  -ncbi-tools-20050605-r1.ebuild:
+  Removed buggy version.
 
 *ncbi-tools-20050605-r2 (14 Dec 2005)
 
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 815b8a9babb4..2ffd558cad43 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,11 +1,9 @@
-MD5 341e528c6a735c9be890ad61e5316155 ncbi-tools-20050605-r1.ebuild 6191
-MD5 9315c657c5b2919039e9f8cfb69efa75 ncbi-tools-20050605-r2.ebuild 6426
-MD5 27f1ef207c35088c37ca584b6158bd03 ncbi-tools-20050605.ebuild 5688
-MD5 97dda37043fa60ee84ade7ca2eb3c4b1 ChangeLog 8906
-MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
-MD5 2f82cbf863fc3fc2522b55f74f9c3244 files/digest-ncbi-tools-20050605-r1 207
-MD5 2f82cbf863fc3fc2522b55f74f9c3244 files/digest-ncbi-tools-20050605-r2 207
-MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
-MD5 9cef4ca17113d005c44d3bf3d330f747 files/digest-ncbi-tools-20050605 144
+MD5 8d2365293a75e6657b3a48dc0f4570f4 ChangeLog 9019
 MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
+MD5 9cef4ca17113d005c44d3bf3d330f747 files/digest-ncbi-tools-20050605 144
+MD5 2f82cbf863fc3fc2522b55f74f9c3244 files/digest-ncbi-tools-20050605-r2 207
 MD5 6b62beda180ee6d7d4d4a52507acc3ff files/ncbi-tools-20050605-lop.patch 701
+MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
+MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
+MD5 9315c657c5b2919039e9f8cfb69efa75 ncbi-tools-20050605-r2.ebuild 6426
+MD5 27f1ef207c35088c37ca584b6158bd03 ncbi-tools-20050605.ebuild 5688
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r1 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r1
deleted file mode 100644
index 416d3489a46f..000000000000
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 61864b4999390eb69e60734b3b02c149 ncbi-tools-20050605.tar.gz 14458684
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
-MD5 76a5f1b547b40dcb00ae3790579dba1b mpiBLAST-1.4.0.tgz 344877
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20050605-r1.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605-r1.ebuild
deleted file mode 100644
index 3f00d98e78b4..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20050605-r1.ebuild
+++ /dev/null
@@ -1,192 +0,0 @@
-# Copyright 1999-2005 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-r1.ebuild,v 1.3 2005/11/16 16:52:54 ribosome 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 ~ppc-macos ~ppc64 ~sparc ~x86"
-IUSE="doc mpi X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	mpi? ( virtual/mpi )
-	X? ( virtual/x11
-		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 "${FILESDIR}"/${P}-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
-	mv "${S}"/bin/*.REAL "${S}"/real
-
-	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 "${S}"/bin/*
-	dolib "${S}"/lib/*
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi
-
-	if use mpi; then
-		cd "${WORKDIR}"/mpiblast-1.4.0
-		make install DESTDIR="${D}" || die
-	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}}
-	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs
-	newdoc "${S}"/config/README README.config
-	newdoc "${S}"/network/encrypt/README README.encrypt
-	newdoc "${S}"/network/nsclilib/readme README.nsclilib
-	newdoc "${S}"/sequin/README README.sequin
-	doman "${S}"/doc/man/*
-
-	# Hypertext user documentation
-	dohtml "${S}"/{README.html,doc/{*.html *.gif}}
-	insinto /usr/share/doc/${PF}/html/blast
-	doins "${S}"/doc/blast/*
-
-	# Developer documentation
-	if use doc; then
-		# "socks" documentation
-		SOCKS="network/socks/socks.cstc.4.2"
-		insinto /usr/share/doc/${PF}/socks
-		doins "${S}"/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects}
-		newins "${S}"/${SOCKS}/libident/README README.libident
-		doins "${S}"/${SOCKS}/sockd/sockd.conf.sample
-		doman "${S}"/${SOCKS}/{doc/*.{1,5,8},libident/ident.3}
-		# "regexp" documentation
-		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/*
-		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo
-		mv "${S}"/regexp/demo "${D}"/usr/share/ncbi/demo/regexp
-		mv "${S}"/regexp/test "${D}"/usr/share/ncbi/demo/regexp/test
-	fi
-
-	# Shared data (similarity matrices and such) and database directory.
-	insinto /usr/share/ncbi/data
-	doins "${S}"/data/*
-	dodir /usr/share/ncbi/formatdb
-
-	# Default config file to set the path for shared data.
-	insinto /etc/ncbi
-	newins "${FILESDIR}"/ncbirc .ncbirc
-
-	# Env file to set the location of the config file and BLAST databases.
-	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
-}