Pruned old version. Added 20080302 to x86 and amd64 (fixed bug #218233).

(Portage version: 2.1.4.4)

3 files changed, 7 insertions, 172 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index d71a45a9227a..2164c7ee6dcd 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.61 2008/04/15 01:21:30 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.62 2008/04/22 00:22:03 ribosome Exp $
+
+  22 Apr 2008; Olivier Fisette <ribosome@gentoo.org>
+  -ncbi-tools-20050605.ebuild, ncbi-tools-20080302.ebuild:
+  Pruned old version. Added 20080302 to x86 and amd64 (fixes bug #218233).
 
 *ncbi-tools-20080302 (15 Apr 2008)
 
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
deleted file mode 100644
index 743d24322663..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
+++ /dev/null
@@ -1,169 +0,0 @@
-# Copyright 1999-2007 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 1.14 2007/10/13 23:09:17 je_fro 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 )"
-
-SLOT="0"
-KEYWORDS="alpha amd64 ppc ppc64 sparc x86"
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	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 ${A}
-
-	use ppc64 && cd "${S}" && epatch "${FILESDIR}/${PN}-lop.patch"
-
-	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"
-}
-
-src_install() {
-	dobin "${S}/bin/*"
-	dolib "${S}/lib/*"
-	mkdir -p "${D}/usr/include/ncbi"
-	cp -RL "${S}/include/*" "${D}/usr/include/ncbi"
-
-	# 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
-}
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
index e0b5b49b6a10..22750344607e 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild,v 1.1 2008/04/15 01:21:30 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild,v 1.2 2008/04/22 00:22:03 ribosome Exp $
 
 inherit flag-o-matic toolchain-funcs eutils autotools
 
@@ -13,7 +13,7 @@ SRC_URI="mirror://gentoo/${P}.tar.gz
 #	mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz )
 
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
+KEYWORDS="~alpha amd64 ~ppc ~ppc64 ~sparc x86"
 
 # IUSE="doc mpi X"
 # mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release.