sci-biology/ncbi-tools: Dropped old

Package-Manager: portage-2.2.0_alpha101/cvs/Linux x86_64

4 files changed, 14 insertions, 201 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 16fe3202c6e6..5ac1d01e4842 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/ncbi-tools
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.82 2010/11/15 21:07:43 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.83 2012/04/26 16:08:36 jlec Exp $
+
+  26 Apr 2012; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild,
+  -ncbi-tools-20090809-r2.ebuild:
+  Dropped old
 
   15 Nov 2010; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild,
   ncbi-tools-20090809-r2.ebuild, ncbi-tools-20100808.ebuild:
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
index fb22b57d8032..898564ba625a 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 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 1.7 2010/11/15 21:07:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild,v 1.8 2012/04/26 16:08:36 jlec Exp $
 
 EAPI=1
 
@@ -148,7 +148,7 @@ src_compile() {
 #		cd "${WORKDIR}"/mpiblast
 #		AM_OPT="-a"
 #		eautoreconf
-#		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
+#		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr
 #		emake || die
 #	fi
 }
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20090809-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20090809-r2.ebuild
deleted file mode 100644
index 92a72c42d024..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20090809-r2.ebuild
+++ /dev/null
@@ -1,191 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20090809-r2.ebuild,v 1.4 2010/11/15 21:07:43 jlec Exp $
-
-EAPI="3"
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-# IUSE=mpi deprecated, use sci-biology/mpiblast separately
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	X? ( >=x11-libs/openmotif-2.3:0 )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
-	echo
-	ewarn 'Please note that the NCBI toolkit (and especially the X'
-	ewarn 'applications) are known to have compilation and run-time'
-	ewarn 'problems when compiled with agressive compilation flags. The'
-	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
-	ewarn 'X support is enabled.'
-	echo
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-extra_vib.patch
-
-	if use ppc || use ppc64; then
-		epatch "${FILESDIR}"/${PN}-lop.patch
-	fi
-
-	if ! use X; then
-		cd "${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} ${LDFLAGS}/" \
-		-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} ${LDFLAGS}/" \
-		-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} ${LDFLAGS}/" \
-		-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} ${LDFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i ppclinux.ncbi.mk || die
-	# ... on generic 64-bit Linux...
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \
-		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
-		-i linux64.ncbi.mk || die
-	# ... on generic Linux.
-	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
-		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \
-		-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 64-bit Linux...
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die
-	# ... on generic Linux.
-	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# We use dynamic libraries
-	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
-	sed \
-		-re "s:/usr(/bin/.*sh):\1:g" \
-		-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
-		-i $(find "${S}" -type f) || die
-}
-
-src_compile() {
-	export EXTRA_VIB
-	cd "${WORKDIR}"
-	csh ncbi/make/makedis.csh || die
-	mkdir "${S}"/cgi
-	mkdir "${S}"/real
-	mv "${S}"/bin/*.cgi "${S}"/cgi || die
-	mv "${S}"/bin/*.REAL "${S}"/real || die
-	cd "${S}"/demo
-	emake \
-		-f ../make/makenet.unx \
-		CC="$(tc-getCC) ${CFLAGS} -I../include  -L../lib" \
-		LDFLAGS="${LDFLAGS}" \
-		spidey || die
-	cp spidey ../bin/ || die
-}
-
-src_install() {
-	dobin "${S}"/bin/* || die "Failed to install binaries."
-	for i in ${EXTRA_VIB}; do
-		dobin "${S}"/build/${i} || die "Failed to install binaries."
-	done
-	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${ED}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-	# TODO: wwwblast with webapps
-	#insinto /usr/share/ncbi/lib/cgi
-	#doins ${S}/cgi/*
-	#insinto /usr/share/ncbi/lib/real
-	#doins ${S}/real/*
-
-	# Basic documentation
-	dodoc "${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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
-	# Developer documentation
-	if use doc; then
-		# Demo programs
-		mkdir "${ED}"/usr/share/ncbi
-		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || 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."
-}
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
index eeb8d92db491..36ea80a4e590 100644
--- a/sci-biology/tree-puzzle/Manifest
+++ b/sci-biology/tree-puzzle/Manifest
@@ -2,13 +2,13 @@
 Hash: SHA512
 
 DIST tree-puzzle-5.2.tar.gz 875142 RMD160 8a69f5ab2ad56a05c0faa6cd02e344c19271bf7a SHA1 fd52a9f04dc871b765d9f7464f68bdb8edc22e37 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb
-EBUILD tree-puzzle-5.2.ebuild 1398 RMD160 d157e66bd7e305517609b7a14719b3972aba2e83 SHA1 5dcd2b638e14c8278c863948d470c7e6248d7133 SHA256 43ae57b37850399cc8345404ad1fc350492e6ededcc357e0f29726f23f34ffda
-MISC ChangeLog 2932 RMD160 b3786d3fdb4a89ec273961b0c6e944fc8576ba1c SHA1 b8fdd409bad129a693151bbc23cfb9843870a855 SHA256 2e0ee14c045c0f73b60e4b60205c3d71efa65d3b770e1657907943e10aae8221
+EBUILD tree-puzzle-5.2.ebuild 1402 RMD160 412d545e43b9a51159c1a33800f4023bd33d900a SHA1 fd541092c8739ac5c5909eda4224d9a877fba08e SHA256 e0b1c41f734ba674cac37e2baa2a73935ab08f70f45aac27c33724dcbd17ca62
+MISC ChangeLog 3025 RMD160 c61be2847464adcf4f7edb11748998ac902fa316 SHA1 3586def3d3bb0f33d89bbc4d15e46480e054bc00 SHA256 17316e6465f77e0429007ecbffa738b01b730309ab29ba3135dcd783b46f3b8c
 MISC metadata.xml 1459 RMD160 1fd787e9bb6887264319e3484e30fd3612b855e0 SHA1 e3bcb0cffa751c79b5c61cb38e8006f368bd01d2 SHA256 ccefdd7d49206f9e090218494a5857e711977a75f24136f3916a34d4dab6219d
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
 
-iEYEAREKAAYFAk+ZcpkACgkQgAnW8HDreRZR3wCglHKTDb183XIpwJA7zcWn/Pja
-tZoAnAwHtj4lBU8WhGjAuCx0oqjTuDDV
-=/c0y
+iEYEAREKAAYFAk+ZcwkACgkQgAnW8HDreRbD0ACginlMRkrAiqz+3jmbuQ3cU1Lg
+ceAAn3ygks8ghDfxEKh652tgD7rTVsgY
+=jJmW
 -----END PGP SIGNATURE-----