Import from Science overlay

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

5 files changed, 92 insertions, 0 deletions

diff --git a/sci-biology/pilercr/ChangeLog b/sci-biology/pilercr/ChangeLog
new file mode 100644
index 000000000000..762520722d77
--- /dev/null
+++ b/sci-biology/pilercr/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/piler-cr
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/pilercr/ChangeLog,v 1.1 2009/07/25 21:41:49 weaver Exp $
+
+  25 Jul 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/pilercr-1.0-gcc43.patch, +metadata.xml:
+  Import from Science overlay
+
+  18 Feb 2009; weaver <weaver@gentoo.org> ChangeLog:
+  New package sci-biology/pilercr, ebuild written by me
+
diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest
new file mode 100644
index 000000000000..2c73c3a4ee97
--- /dev/null
+++ b/sci-biology/pilercr/Manifest
@@ -0,0 +1,5 @@
+AUX pilercr-1.0-gcc43.patch 854 RMD160 b10c529c27fa821b0a6d0aac9bfb1f3b42d0c3d3 SHA1 c432e0a8dadaff8b216f398a6e97d4be26a88de0 SHA256 ee86cf9ad7ab5f18f9d06673c930d4c72f1e387c5b5fccc81044edbf613d7123
+DIST pilercr-1.0.tar.gz 1709144 RMD160 9dc295222f58e9134a88865ac6465678de6e3f20 SHA1 d91d173660c004c32017290c1ffb86930a179d67 SHA256 75f58d58567c478e271c4c554071a7d6d642e6daef8981ee2618daa7b53fa923
+EBUILD pilercr-1.0.ebuild 748 RMD160 1d49151bc3e113ddec4d157809c38a4d9d429d83 SHA1 a0accccd03604b19713af040910ef02e204c004e SHA256 9c206807e69b6be6c7a19b688ba5e5173784c249f2b54c74269329e9294c3159
+MISC ChangeLog 452 RMD160 861872e24b6fad4fa8b5bfb721521a6eff5b33f3 SHA1 e7bf8cbb8e5caace049f294ea4c516a4dfefac8e SHA256 6a1204a3dacfdcb7ec0b668b72390afaa63d32226a5f036fd4678ce5b1602d66
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
new file mode 100644
index 000000000000..7b49df872e27
--- /dev/null
+++ b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
@@ -0,0 +1,33 @@
+diff -dur work/multaln.h work-orig/multaln.h
+--- work/multaln.h	2007-04-17 19:02:18.000000000 +0000
++++ work-orig/multaln.h	2009-02-18 21:25:26.166333299 +0000
+@@ -6,6 +6,7 @@
+ #define _CRT_SECURE_NO_DEPRECATE	1

+ #endif

+ 

++#include <cstring>

+ #include <vector>

+ #include <limits.h>

+ #include <ctype.h>

+diff -dur work/seqvect.h work-orig/seqvect.h
+--- work/seqvect.h	2006-04-06 23:36:18.000000000 +0000
++++ work-orig/seqvect.h	2009-02-18 21:25:26.171090246 +0000
+@@ -1,6 +1,7 @@
+ #ifndef SeqVect_h

+ #define SeqVect_h

+ 

++#include <stdio.h>

+ #include <vector>

+ #include "seq.h"

+ 

+diff -dur work/tree.h work-orig/tree.h
+--- work/tree.h	2006-04-05 23:52:42.000000000 +0000
++++ work-orig/tree.h	2009-02-18 21:25:26.171090246 +0000
+@@ -1,6 +1,7 @@
+ #ifndef tree_h

+ #define tree_h

+ 

++#include <stdlib.h>

+ #include <limits.h>

+ 

+ class Clust;

diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/pilercr/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/pilercr/pilercr-1.0.ebuild b/sci-biology/pilercr/pilercr-1.0.ebuild
new file mode 100644
index 000000000000..043b9400cb6c
--- /dev/null
+++ b/sci-biology/pilercr/pilercr-1.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/pilercr/pilercr-1.0.ebuild,v 1.1 2009/07/25 21:41:49 weaver Exp $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Analysis of repetitive DNA found in genome sequences"
+HOMEPAGE="http://www.drive5.com/pilercr/"
+#SRC_URI="http://www.drive5.com/pilercr/pilercr.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc43.patch || die
+}
+
+src_compile() {
+	emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die
+}
+
+src_install() {
+	dobin pilercr || die
+}