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

Package-Manager: portage-2.1.4.4

4 files changed, 9 insertions, 176 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/Manifest b/sci-biology/ncbi-tools/Manifest
index e4e9e624a3fd..958562a4b16e 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -4,16 +4,14 @@ AUX ncbi-tools-extra_vib.patch 1393 RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a
 AUX ncbi-tools-lop.patch 701 RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 SHA1 be28d340be72b9840342b407d95dc2a558e39de9 SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc
 AUX ncbirc 33 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 SHA1 eb14976d464f4fa0e14085c8dd58886b0c684a56 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e
 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-20070826.tar.gz 17076175 RMD160 00daadd503bf729c15ada0008e305492a076fe15 SHA1 5e61f4f73ef52d145d0df86bb00f03f2db833ee9 SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8
 DIST ncbi-tools-20080302.tar.gz 17294669 RMD160 e269bcadc9e498163252e348a314bab8d0ece8f6 SHA1 d91a66bafac62dd07cc2e524874492388e5a780d SHA256 93a30ec0a6e408858c6364039a4eb240d9fadaf8ce670a14151e03c5169a12c1
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
-EBUILD ncbi-tools-20050605.ebuild 5749 RMD160 b44f50468496fd8091515b899d9bc5971db646a3 SHA1 673c0f66d0d2a46b86c5dbcfd2c74d751f531450 SHA256 ff797954513ff7e293ab3519642e0864b781233a7bf15fe5eb98345c8a3c02f5
 EBUILD ncbi-tools-20060507.ebuild 6406 RMD160 0d52953dc8cff30b92a68fe9a726f19297f7d72d SHA1 4101fa84b7ab60c58ffb42f0b05bd895f5ab6937 SHA256 2653da742470eb3cc79541cdd745af2f858bbd0356ce141b88cc3e1dd07ad9a6
 EBUILD ncbi-tools-20061015-r1.ebuild 6495 RMD160 24ab84b6a4bce25a0571c78a5489d5725e81a01b SHA1 e409498fc64031e0208fb5299d377217670a0759 SHA256 135d19e95452b5662a9751f4101ef17a66a618c3031894bb2aa8f761d64a85ad
 EBUILD ncbi-tools-20070826.ebuild 7123 RMD160 331d2e7cac864d2e6582c9beaa7ae1af08da548c SHA1 34e83e093b7cdc49950732fad52664b3a1896593 SHA256 fbefd6e0e7f4f3c96d9f162cdee8e43a1ba3e9ed40c6eb19303509b836cb0241
-EBUILD ncbi-tools-20080302.ebuild 7120 RMD160 b77bd75ba37bd3e6386624101289cf97b4bfbbee SHA1 9eefb56598fc1b24f49667cf528b6eb12d94b7a1 SHA256 0b256f5ab7064574a9affee45c6966e9c273bbe2c36e8d21605987bcfd2bd0fa
-MISC ChangeLog 13384 RMD160 e241ea1b0049add5636e72ef18162b3da4ae447a SHA1 0fe45ca85b856528eb36d8f016b49fdf1bbfeef4 SHA256 ec517a32a120a93f9623b6c4b264241dea0de14cc8448c90e2118ecaf426f98a
+EBUILD ncbi-tools-20080302.ebuild 7120 RMD160 f1bfecf895ebf4dfceb5e44596c3c3a51a371609 SHA1 b0929c6bd0793952309cb1ac55868d24f1044f5f SHA256 a647313fd8fa97da14c743526dcae0ec6a9f4685e6a4d30c6634f122bbbfb544
+MISC ChangeLog 13574 RMD160 435bb85c6cf86df68b2b0556eaf8e0fa2e3185e2 SHA1 004b1c7ccb55e16b5ba8b7dd9381cccf1d91a2ce SHA256 cd7003ed5a11fb69c958e68e59796fa62120fdb2d5c9b1967486977b297bcfc6
 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
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.