Fixed file collisions with "dev-libs/libpcre" (bug #115463)

(Portage version: 2.0.51.22-r3)

4 files changed, 207 insertions, 1 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index afad1415679f..79351828b3c0 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.35 2005/11/16 16:52:54 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.36 2005/12/14 20:24:03 ribosome Exp $
+
+*ncbi-tools-20050605-r2 (14 Dec 2005)
+
+  14 Dec 2005; Olivier Fisette <ribosome@gentoo.org>
+  +ncbi-tools-20050605-r2.ebuild:
+  Fixed file collisions with "dev-libs/libpcre" (bug #115463).
 
   16 Nov 2005; Olivier Fisette <ribosome@gentoo.org>
   ncbi-tools-20050605-r1.ebuild:
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 4be4b4b9f7a2..dee54a51dc57 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,8 +1,10 @@
 MD5 341e528c6a735c9be890ad61e5316155 ncbi-tools-20050605-r1.ebuild 6191
+MD5 0c7342e27db53e3b3afb7abd3bccb71b ncbi-tools-20050605-r2.ebuild 6432
 MD5 27f1ef207c35088c37ca584b6158bd03 ncbi-tools-20050605.ebuild 5688
 MD5 93fad815644e31ea1a4a8a2f48699055 ChangeLog 8716
 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 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
new file mode 100644
index 000000000000..416d3489a46f
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
@@ -0,0 +1,3 @@
+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-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
new file mode 100644
index 000000000000..48724ff87ce3
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20050605-r2.ebuild
@@ -0,0 +1,195 @@
+# 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-r2.ebuild,v 1.1 2005/12/14 20:24:03 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 || die
+	mv "${S}"/bin/*.REAL "${S}"/real || die
+
+	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 "${S}"/bin/* || die
+	dolib "${S}"/lib/* || die
+	mkdir -p "${D}"/usr/include/ncbi
+	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || die
+
+	if use mpi; then
+		cd "${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}} || die
+	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || die
+	newdoc "${S}"/config/README README.config || die
+	newdoc "${S}"/network/encrypt/README README.encrypt || die
+	newdoc "${S}"/network/nsclilib/readme README.nsclilib || die
+	newdoc "${S}"/sequin/README README.sequin || die
+	doman "${S}"/doc/man/* || die
+
+	# Hypertext user documentation
+	dohtml "${S}"/{README.html,doc/{*.html *.gif}} || die
+	insinto /usr/share/doc/${PF}/html/blast || die
+	doins "${S}"/doc/blast/* || die
+
+	# Developer documentation
+	if use doc; then
+		# "socks" documentation
+		SOCKS="network/socks/socks.cstc.4.2"
+		insinto /usr/share/doc/${PF}/socks
+		doins "${S}"/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects} || die
+		newins "${S}"/${SOCKS}/libident/README README.libident
+		doins "${S}"/${SOCKS}/sockd/sockd.conf.sample || die
+		doman "${S}"/${SOCKS}/{doc/*.{1,5,8},libident/ident.3} || die
+
+		# "regexp" documentation (No longer installed, see bug #115463.)
+		# 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/* || die
+
+		# Demo programs
+		mkdir "${D}"/usr/share/ncbi
+		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
+		mv "${S}"/regexp/demo "${D}"/usr/share/ncbi/demo/regexp || die
+		mv "${S}"/regexp/test "${D}"/usr/share/ncbi/demo/regexp/test || die
+	fi
+
+	# Shared data (similarity matrices and such) and database directory.
+	insinto /usr/share/ncbi/data
+	doins "${S}"/data/* || die
+	dodir /usr/share/ncbi/formatdb || die
+
+	# Default config file to set the path for shared data.
+	insinto /etc/ncbi
+	newins "${FILESDIR}"/ncbirc .ncbirc || die
+
+	# Env file to set the location of the config file and BLAST databases.
+	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die
+}