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

10 files changed, 270 insertions, 0 deletions

diff --git a/sci-libs/libghemical/Manifest b/sci-libs/libghemical/Manifest
new file mode 100644
index 000000000000..e95eb151f36e
--- /dev/null
+++ b/sci-libs/libghemical/Manifest
@@ -0,0 +1,3 @@
+DIST libghemical-2.00.tar.gz 629479 SHA256 e873b3042df75fa1c9f37fc99f2ff14227965ed13c7680169f714ab6575d5f21
+DIST libghemical-2.99.1.tar.gz 778812 SHA256 f9b6df3c1e98a524f90644ebaaebb804792f391ca383c0f92b609060dc485d9f
+DIST libghemical-3.0.0.tar.gz 787947 SHA256 db8c3add0aa1f94c21016d60fa3f66fb194e56b8e9fceaa3860c603700efc3ac SHA512 71531e7bd72a7fa063dd35536a346f15e3c0fd0284112fa2f304580204b93552bd0c9a426cee22044b5dd1662e34e5d191d20af938e474561fe55f2394e7519e WHIRLPOOL fae8e49a2136460013296e0a23a56513a36941ece73013a1a21b530abdfbabfba2b5098457b70a9cd1694759995ffeae01250d05034e0c1186fd2f47af52af08
diff --git a/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch b/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch
new file mode 100644
index 000000000000..bef730abbe4c
--- /dev/null
+++ b/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch
@@ -0,0 +1,24 @@
+diff -urN libghemical-2.00.orig/configure.ac libghemical-2.00/configure.ac
+--- libghemical-2.00.orig/configure.ac	2006-05-12 23:31:06.000000000 -0700
++++ libghemical-2.00/configure.ac	2006-05-12 23:54:20.000000000 -0700
+@@ -69,8 +69,18 @@
+ AC_CHECK_LIB([m], [acos])
+ 
+ if test $WITH_MPQC = yes; then
+-	AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
+-	AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
++	AC_CHECK_LIB([blas], [dgemm_], HAVE_BLAS="yes", , -lpthread)
++	AC_CHECK_LIB([blas], [dgemm], HAVE_BLAS="yes", , -lpthread)
++	AC_CHECK_LIB([blas], [dgemm__], HAVE_BLAS="yes", , -lpthread)
++	if test "x${HAVE_BLAS}" = "x"; then
++		AC_MSG_ERROR([Cannot find blas library needed for MPQC support])
++	fi
++	AC_CHECK_LIB([lapack], [cheev_], HAVE_LAPACK="yes", , -lpthread)
++	AC_CHECK_LIB([lapack], [cheev], HAVE_LAPACK="yes", , -lpthread)
++	AC_CHECK_LIB([lapack], [cheev__], HAVE_LAPACK="yes", , -lpthread)
++	if test "x${HAVE_LAPACK}" = "x"; then
++		AC_MSG_ERROR([Cannot find lapack library needed for MPQC support])
++	fi
+ 	AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no")
+ 	if test "${HAVE_MPQC}" = "yes"; then
+ 		AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC])
diff --git a/sci-libs/libghemical/files/libghemical-2.98-gcc43.patch b/sci-libs/libghemical/files/libghemical-2.98-gcc43.patch
new file mode 100644
index 000000000000..d92d31d93b74
--- /dev/null
+++ b/sci-libs/libghemical/files/libghemical-2.98-gcc43.patch
@@ -0,0 +1,43 @@
+--- src/atom.h.orig	2008-06-09 03:59:34.262567972 -0500
++++ src/atom.h	2008-06-09 04:00:07.136698792 -0500
+@@ -10,6 +10,8 @@
+ #ifndef ATOM_H
+ #define ATOM_H
+ 
++#include <cstdlib>
++#include <cstring>
+ #include "libghemicaldefine.h"
+ #include "libghemicalconfig2.h"
+ 
+--- src/notice.h.orig	2008-06-09 04:00:24.472509840 -0500
++++ src/notice.h	2008-06-09 04:00:44.608265748 -0500
+@@ -10,6 +10,7 @@
+ #ifndef NOTICE_H
+ #define NOTICE_H
+ 
++#include <cstring>
+ #include "libghemicaldefine.h"
+ #include "libghemicalconfig2.h"
+ 
+--- src/sasaeval.cpp	2008-08-01 09:39:01.000000000 +0530
++++ src/sasaeval.cpp	2008-08-01 09:40:33.000000000 +0530
+@@ -21,6 +21,9 @@
+ #include "sasaeval.h"
+
+ #include "engine.h"
++#include <vector>
++#include <algorithm>
++using namespace std;
+
+ // the surface area code apparently contains some bugs, since it sometimes
+ // crashes. another possibility is that the surface area math contains some
+--- src/sasaeval.h	2008-07-31 00:40:08.000000000 +0530
++++ src/sasaeval.h	2008-08-01 09:40:04.000000000 +0530
+@@ -24,6 +24,7 @@
+ #define SASAEVAL_H
+
+ #include "typedef.h"
++#include <stdlib.h>
+
+ struct cg_nbt3_nl;	// SASA neighbor list.
+
diff --git a/sci-libs/libghemical/files/libghemical-2.98-gl.patch b/sci-libs/libghemical/files/libghemical-2.98-gl.patch
new file mode 100644
index 000000000000..8cea8aab636e
--- /dev/null
+++ b/sci-libs/libghemical/files/libghemical-2.98-gl.patch
@@ -0,0 +1,13 @@
+diff --git a/src/typedef.h b/src/typedef.h
+index 8d2efcc..1e304e8 100644
+--- a/src/typedef.h
++++ b/src/typedef.h
+@@ -27,7 +27,7 @@
+ 
+ // comment this out if you have no GL/gl.h available...
+ 
+-#define HAVE_GL_H	// 2008-07-31 ; also with mingw comment this out???
++// #define HAVE_GL_H	// 2008-07-31 ; also with mingw comment this out??? 
+ 
+ // added by Robert Williams for Compaq cxx, alpha 11/28/01
+ 
diff --git a/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch b/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch
new file mode 100644
index 000000000000..ad46079e945d
--- /dev/null
+++ b/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch
@@ -0,0 +1,26 @@
+diff --git a/configure.ac b/configure.ac
+index b01e5fa..943890b 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -151,7 +151,7 @@ fi
+ # Checks for header files.
+ # ^^^^^^^^^^^^^^^^^^^^^^^^
+ 
+-AC_CHECK_HEADERS([GL/gl.h])
++# AC_CHECK_HEADERS([GL/gl.h])
+ 
+ # Checks for typedefs, structures, and compiler characteristics.
+ # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+diff --git a/src/typedef.h b/src/typedef.h
+index 8d2efcc..0ba62fe 100644
+--- a/src/typedef.h
++++ b/src/typedef.h
+@@ -27,7 +27,7 @@
+ 
+ // comment this out if you have no GL/gl.h available...
+ 
+-#define HAVE_GL_H	// 2008-07-31 ; also with mingw comment this out???
++// #define HAVE_GL_H	// 2008-07-31 ; also with mingw comment this out???
+ 
+ // added by Robert Williams for Compaq cxx, alpha 11/28/01
+ 
diff --git a/sci-libs/libghemical/files/libghemical-gcc43.patch b/sci-libs/libghemical/files/libghemical-gcc43.patch
new file mode 100644
index 000000000000..53db5fba4d90
--- /dev/null
+++ b/sci-libs/libghemical/files/libghemical-gcc43.patch
@@ -0,0 +1,21 @@
+--- src/atom.h.orig	2008-06-09 03:59:34.262567972 -0500
++++ src/atom.h	2008-06-09 04:00:07.136698792 -0500
+@@ -10,6 +10,8 @@
+ #ifndef ATOM_H
+ #define ATOM_H
+ 
++#include <cstdlib>
++#include <cstring>
+ #include "libghemicaldefine.h"
+ #include "libghemicalconfig2.h"
+ 
+--- src/notice.h.orig	2008-06-09 04:00:24.472509840 -0500
++++ src/notice.h	2008-06-09 04:00:44.608265748 -0500
+@@ -10,6 +10,7 @@
+ #ifndef NOTICE_H
+ #define NOTICE_H
+ 
++#include <cstring>
+ #include "libghemicaldefine.h"
+ #include "libghemicalconfig2.h"
+ 
diff --git a/sci-libs/libghemical/libghemical-2.00.ebuild b/sci-libs/libghemical/libghemical-2.00.ebuild
new file mode 100644
index 000000000000..7e7c489336e4
--- /dev/null
+++ b/sci-libs/libghemical/libghemical-2.00.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+inherit autotools eutils
+
+DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
+HOMEPAGE="http://bioinformatics.org/ghemical/"
+SRC_URI="http://www.bioinformatics.org/ghemical/download/${P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ppc x86"
+IUSE="mopac7 mpqc"
+RDEPEND="mopac7? ( sci-chemistry/mopac7 )
+		mpqc? ( >=sci-chemistry/mpqc-2.3.1-r1
+			virtual/blas
+			virtual/lapack )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+src_unpack() {
+	unpack ${A}
+	epatch "${FILESDIR}"/${PV}-really-find-blas-and-lapack.patch
+	cd "${S}"
+	eautoreconf
+}
+
+src_compile() {
+	econf \
+		$(use_enable mopac7) \
+		$(use_enable mpqc) \
+		|| die "configure failed"
+	emake || die "make failed"
+}
+
+src_install() {
+	make DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-libs/libghemical/libghemical-2.99.1.ebuild b/sci-libs/libghemical/libghemical-2.99.1.ebuild
new file mode 100644
index 000000000000..3c5ebbfe764f
--- /dev/null
+++ b/sci-libs/libghemical/libghemical-2.99.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit autotools eutils
+
+DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
+HOMEPAGE="http://bioinformatics.org/ghemical/"
+SRC_URI="http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE="mopac7 mpqc static-libs"
+
+RDEPEND="
+	mopac7? ( >=sci-chemistry/mopac7-1.13-r1 )
+	mpqc? (
+		>=sci-chemistry/mpqc-2.3.1-r1
+		virtual/blas
+		virtual/lapack )"
+DEPEND="${RDEPEND}
+		virtual/pkgconfig"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gl.patch
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--enable-shared \
+		$(use_enable mopac7) \
+		$(use_enable mpqc) \
+		$(use_enable static-libs static)
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-libs/libghemical/libghemical-3.0.0.ebuild b/sci-libs/libghemical/libghemical-3.0.0.ebuild
new file mode 100644
index 000000000000..d1d3dbf4418f
--- /dev/null
+++ b/sci-libs/libghemical/libghemical-3.0.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="3"
+
+inherit autotools eutils
+
+DESCRIPTION="Chemical quantum mechanics and molecular mechanics"
+HOMEPAGE="http://bioinformatics.org/ghemical/"
+SRC_URI="http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="mopac7 mpqc static-libs"
+
+RDEPEND="
+	mopac7? ( >=sci-chemistry/mopac7-1.13-r1 )
+	mpqc? (
+		>=sci-chemistry/mpqc-2.3.1-r1
+		virtual/blas
+		virtual/lapack )"
+DEPEND="${RDEPEND}
+		virtual/pkgconfig"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-2.98-gl.patch
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--enable-shared \
+		$(use_enable mopac7) \
+		$(use_enable mpqc) \
+		$(use_enable static-libs static)
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "install failed"
+}
diff --git a/sci-libs/libghemical/metadata.xml b/sci-libs/libghemical/metadata.xml
new file mode 100644
index 000000000000..e94fba7a2bf4
--- /dev/null
+++ b/sci-libs/libghemical/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<longdescription>
+Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models 
+and molecular mechanics models (there is an experimental Tripos 5.2-like force 
+field for organic molecules). Also a tool for reduced protein models is 
+included. Geometry optimization, molecular dynamics and a large set of 
+visualization tools are currently available.
+</longdescription>
+<use>
+  <flag name='mopac7'>Use <pkg>sci-chemistry/mopac7</pkg> for semi-empirical
+    calculations</flag>
+  <flag name='mpqc'>Use <pkg>sci-chemistry/mpqc</pkg> for quantum-mechanical
+    calculations</flag>
+</use>
+</pkgmetadata>