proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 128 insertions, 0 deletions

diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest
new file mode 100644
index 000000000000..0fad882975fa
--- /dev/null
+++ b/sci-biology/last/Manifest
@@ -0,0 +1,2 @@
+DIST last-230.zip 418077 SHA256 8d55ee95e05a08afa72690df9086886e97142adcfbf750cf5cf6015b91215484 SHA512 46c858c2bd4a9aa00ac3b448ce78bdee6c1edd4f6569cff3c81ec8a7c661d89a9b5e7a888cbc6da190b243f0ec83c485b4574dadc6a58669d9b955eb70c329d1 WHIRLPOOL aaa0483a58821cca0fdd7875cb4e7c62493fd724729d957df1d51c7612e92e3acefae2727789f63a248f02c976a45c3209d6bac2c39f54d84f02d1106c2d0f85
+DIST last-299.zip 453159 SHA256 cc68e9c0b5220da67fd0239c9663dc0d1a05e63b337a6c98cfef6d5c38d0c54c SHA512 74e89129cc17482ec1a99e2d940ca62374c130fea2fa53ea7d2c3703b6ca5751f348110909d61562c4839d8fb1793619c2f41c25c8968b3ab53f0c7191f4a00b WHIRLPOOL 12e826c22c2d91845e89aa0c6e99af785973e8a276dec4f97ed292e144327c7c58024622d3f7285c6107bca7af1bf3c29a23ec9d22dc88ff5dc041a0df96f3ce
diff --git a/sci-biology/last/files/162-gcc46.patch b/sci-biology/last/files/162-gcc46.patch
new file mode 100644
index 000000000000..9c66c6d39f00
--- /dev/null
+++ b/sci-biology/last/files/162-gcc46.patch
@@ -0,0 +1,15 @@
+ src/XdropAligner.hh |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/XdropAligner.hh b/src/XdropAligner.hh
+index 9dea32e..3c0e35f 100644
+--- a/src/XdropAligner.hh
++++ b/src/XdropAligner.hh
+@@ -12,6 +12,7 @@
+ #include <vector>
+ #include <cassert>
+ #include <climits>  // INT_MAX
++#include <cstddef>
+ 
+ namespace cbrc{
+ 
diff --git a/sci-biology/last/files/162-ldflags.patch b/sci-biology/last/files/162-ldflags.patch
new file mode 100644
index 000000000000..e5dd3ee2234e
--- /dev/null
+++ b/sci-biology/last/files/162-ldflags.patch
@@ -0,0 +1,16 @@
+ src/makefile |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/src/makefile b/src/makefile
+index e77ffa7..92e4575 100644
+--- a/src/makefile
++++ b/src/makefile
+@@ -51,7 +51,7 @@ lastal: $(ALSRC) $(ALINC) makefile $(OBJ)
+ 	$(CXX) $(STRICT) $(CXXFLAGS) -o $@ $(ALSRC) $(OBJ)
+ 
+ lastex: $(EXSRC) $(EXINC) makefile
+-	$(CXX) -Igumbel_params $(CXXFLAGS) -o $@ $(EXSRC)
++	$(CXX) $(STRICT) -Igumbel_params $(CXXFLAGS) -o $@ $(EXSRC)
+ 
+ $(OBJ): CA_code/*.c CA_code/*.h makefile
+ 	$(CC) $(CFLAGS) -c CA_code/lambda_calculator.c
diff --git a/sci-biology/last/last-230.ebuild b/sci-biology/last/last-230.ebuild
new file mode 100644
index 000000000000..51dc9ee0faf0
--- /dev/null
+++ b/sci-biology/last/last-230.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/archive/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+	sed \
+		-e 's:-o $@:$(LDFLAGS) -o $@:g' \
+		-i src/makefile || die
+}
+
+src_compile() {
+	emake \
+		-e -C src \
+		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		STRICT="" || die
+}
+
+src_install() {
+	dobin src/last{al,db,ex}
+	exeinto /usr/share/${PN}/scripts
+	doexe scripts/*
+	dodoc doc/*.txt ChangeLog.txt README.txt
+}
diff --git a/sci-biology/last/last-299.ebuild b/sci-biology/last/last-299.ebuild
new file mode 100644
index 000000000000..9d32fdf11c3c
--- /dev/null
+++ b/sci-biology/last/last-299.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils toolchain-funcs python-r1
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+	sed \
+		-e 's:-o $@:$(LDFLAGS) -o $@:g' \
+		-i src/makefile || die
+}
+
+src_compile() {
+	emake \
+		-e -C src \
+		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		STRICT="" || die
+}
+
+src_install() {
+	local i
+
+	dobin src/last{al,db,ex}
+
+	dodoc doc/*.txt ChangeLog.txt README.txt
+	dohtml doc/*html
+
+	cd scripts || die
+	for i in *py; do
+		python_parallel_foreach_impl python_newscript ${i} ${i%.py}
+	done
+	dobin *sh
+}
diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/last/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>