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

4 files changed, 70 insertions, 0 deletions

diff --git a/sci-biology/mammoth/Manifest b/sci-biology/mammoth/Manifest
new file mode 100644
index 000000000000..584405eb5350
--- /dev/null
+++ b/sci-biology/mammoth/Manifest
@@ -0,0 +1 @@
+DIST mammoth-1.0-src.tgz 319617 SHA256 7a21bc47db4a47cc5ebeeb4c46761a79eece0a802104a3d6189f388a03e59de2
diff --git a/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch
new file mode 100644
index 000000000000..63bf9f246750
--- /dev/null
+++ b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch
@@ -0,0 +1,21 @@
+http://gcc.gnu.org/onlinedocs/gcc-4.2.2/gfortran/SYSTEM.html#SYSTEM
+
+This intrinsic is provided in both subroutine and function forms; 
+however, only one form can be used in any given program unit.
+
+--- src/6apply_rot_tras.f.orig	2007-12-10 00:51:35.000000000 -0800
++++ src/6apply_rot_tras.f	2007-12-10 00:55:07.000000000 -0800
+@@ -47,11 +47,11 @@
+       endif
+ 
+ 
+-      call system ('echo $PWD > junk1')
++      i = system ('echo $PWD > junk1')
+       open(unit=21,file='junk1')
+       read(21,'(a340)', end=7) path
+  7    close(21)
+-      call system ('rm -f junk1')
++      i = system ('rm -f junk1')
+ 
+ c      write(6,*)'my path is ', path
+ c      write(6,*)tras1,tras2,tras3,
diff --git a/sci-biology/mammoth/mammoth-1.0-r1.ebuild b/sci-biology/mammoth/mammoth-1.0-r1.ebuild
new file mode 100644
index 000000000000..750d95dd894b
--- /dev/null
+++ b/sci-biology/mammoth/mammoth-1.0-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools eutils fortran-2 flag-o-matic toolchain-funcs
+
+MY_P="${P}-src"
+
+DESCRIPTION="MAtching Molecular Models Obtained from THeory"
+HOMEPAGE="http://ub.cbm.uam.es/software.php"
+SRC_URI="${MY_P}.tgz"
+
+LICENSE="mammoth"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+S=${WORKDIR}/${MY_P}
+
+pkg_nofetch() {
+	einfo "Download the source code for MAMMOTH from"
+	einfo "${HOMEPAGE}"
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	# Broken with gfortran without this patch
+	epatch "${FILESDIR}"/${PV}-consistent-system-intrinsic.patch
+
+	case $(tc-getFC) in
+		g77)		append-fflags -ffixed-line-length-none ;;
+		gfortran)	append-fflags -ffixed-line-length-none ;;
+	esac
+
+	# It comes with a custom-modified configure for some reason,
+	# which forces you to pass in the Fortran compiler as a parameter.
+	# Let's do the standard stuff instead.
+	eautoreconf
+}
diff --git a/sci-biology/mammoth/metadata.xml b/sci-biology/mammoth/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mammoth/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>