Pruning old versions

Package-Manager: portage-2.0.51.22-r3

7 files changed, 6 insertions, 353 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 4431f104d879..c7832cbcb3af 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 1.30 2005/10/22 16:02:56 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.31 2005/10/22 17:45:46 ribosome Exp $
+
+  22 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -files/21ncbi,
+  -ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild:
+  Pruning old versions.
 
   22 Oct 2005; Fabian Groffen <grobian@gentoo.org>
   ncbi-tools-20050605.ebuild:
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index b848b1e2e952..c44ef5907f39 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,12 +1,7 @@
-MD5 6c8b57dc3b8c8523ae2adb7a1a8f1ed3 ncbi-tools-20041020-r1.ebuild 5630
 MD5 be21ba792698dcaa322cfa98371eadf3 ncbi-tools-20050605.ebuild 5690
-MD5 0cfe991ee8c23a5a862c2386eba988e8 ncbi-tools-20050429.ebuild 5628
-MD5 7d3a037a19b037aff42ab423fabe2a9a ChangeLog 7941
+MD5 3b3a6c467e5443baabdce9d6dec4fd8b ChangeLog 8098
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
-MD5 6fa8c1b5254e9c217c399c949bc75f45 files/digest-ncbi-tools-20041020-r1 144
-MD5 ae77b2436a5f4dfcb6f71f2149782dc7 files/digest-ncbi-tools-20050429 144
 MD5 9cef4ca17113d005c44d3bf3d330f747 files/digest-ncbi-tools-20050605 144
 MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
-MD5 756db6700c84d3b303bfc3d0a28871de files/21ncbi 166
 MD5 6b62beda180ee6d7d4d4a52507acc3ff files/ncbi-tools-20050605-lop.patch 701
diff --git a/sci-biology/ncbi-tools/files/21ncbi b/sci-biology/ncbi-tools/files/21ncbi
deleted file mode 100644
index 1983fe83de02..000000000000
--- a/sci-biology/ncbi-tools/files/21ncbi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Location of the formatdb data sets
-BLASTDB="/usr/share/ncbi/formatdb"
-# Location of the ".ncbi.rc" file which sets the default path for shared data.
-NCBI=/etc/ncbi
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20041020-r1 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20041020-r1
deleted file mode 100644
index de3d6e86a474..000000000000
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20041020-r1
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 3f82bce2a3ce549f055ff989a4b825ed ncbi-tools-20041020.tar.gz 13867811
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050429 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050429
deleted file mode 100644
index 978e30d5b949..000000000000
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050429
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 f814c7b8b433cc479d5aa783a61e21c8 ncbi-tools-20050429.tar.gz 14061320
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20041020-r1.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20041020-r1.ebuild
deleted file mode 100644
index 7bcadc1dbd4c..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20041020-r1.ebuild
+++ /dev/null
@@ -1,169 +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-20041020-r1.ebuild,v 1.5 2005/06/09 10:16:21 corsair Exp $
-
-inherit flag-o-matic toolchain-funcs
-
-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 ppc-macos ppc64 ~sparc x86"
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	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 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=pentiumpro/NCBI_LDFLAGS1 = ${CFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentiumpro/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-20050429.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050429.ebuild
deleted file mode 100644
index fd525265dfa7..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20050429.ebuild
+++ /dev/null
@@ -1,169 +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-20050429.ebuild,v 1.7 2005/09/16 07:19:58 agriffis Exp $
-
-inherit flag-o-matic toolchain-funcs
-
-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 ~ppc-macos -ppc64 ~sparc x86"
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	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 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
-}