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

7 files changed, 258 insertions, 0 deletions

diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest
new file mode 100644
index 000000000000..024410ff1615
--- /dev/null
+++ b/sci-biology/treeviewx/Manifest
@@ -0,0 +1 @@
+DIST tv-0.5.1.tar.gz 426745 RMD160 27c92a0f43c59c8988fe2d1410adb6de429e94c9 SHA1 0b0887477ca0d9ded6d0ee8bef014b6208e1fc14 SHA256 118bdbefb3f21636b1ba9da92e1b2029cb4d7d9944f4d02d2deace4ebb14c2d1
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch
new file mode 100644
index 000000000000..33bd3b1741f6
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch
@@ -0,0 +1,77 @@
+diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp
+--- tv-0.5.1/TreeLib/Parse.cpp	2002-02-23 07:22:32.000000000 -0500
++++ tv-0.5.1.new/TreeLib/Parse.cpp	2008-06-17 06:08:24.000000000 -0400
+@@ -24,6 +24,11 @@
+ #include <ctype.h>
+ #include "Parse.h"
+ 
++
++
++
++#include <cstring>
++
+ // Return the next token in the string
+ tokentype Parser::NextToken ()
+ {
+diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp
+--- tv-0.5.1/TreeLib/TreeLib.cpp	2004-05-13 08:22:11.000000000 -0400
++++ tv-0.5.1.new/TreeLib/TreeLib.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -24,6 +24,8 @@
+ #include "TreeLib.h"
+ #include "Parse.h"
+ 
++
++#include <cstdlib>
+ #include <vector>
+ 
+ 
+diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp
+--- tv-0.5.1/TreeLib/treereader.cpp	2003-09-10 08:58:16.000000000 -0400
++++ tv-0.5.1.new/TreeLib/treereader.cpp	2008-06-17 06:07:15.000000000 -0400
+@@ -28,6 +28,9 @@
+ 	#include <stdlib.h>
+ #endif
+ 
++#include <cstring>
++#include <cstdlib>
++
+ //------------------------------------------------------------------------------
+ TreeReader::TreeReader (Tokeniser &p) : parser (p)
+ {
+diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp
+--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp	2002-12-10 06:35:49.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp
+--- tv-0.5.1/ncl-2.0/src/nexus.cpp	2002-12-10 06:35:50.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp
+--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp	2005-04-29 10:28:17.000000000 -0400
++++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,5 @@
++
++#include <cstring>
+ #include "nexusdefs.h"
+ #include "xnexus.h"
+ #include "nexustoken.h"
+diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp
+--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp	2001-02-02 07:55:40.000000000 -0500
++++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp	2008-06-17 05:58:17.000000000 -0400
+@@ -1,3 +1,6 @@
++
++#include <cstring>
++
+ #ifdef __BORLANDC__
+ 	// Undefine __MINMAX_DEFINED so that min and max are correctly defined
+ 	#ifdef __MINMAX_DEFINED
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch
new file mode 100644
index 000000000000..e3ba6b2fff50
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch
@@ -0,0 +1,14 @@
+Fix build w/ wxGTK-2.8
+http://bugs.debian.org/567238
+
+--- a/tview.cpp
++++ b/tview.cpp
+@@ -994,7 +994,7 @@ END_EVENT_TABLE()
+ MyCanvas::MyCanvas(wxView *v, wxMDIChildFrame *frame, const wxPoint& pos, const wxSize& size, long style):
+  wxScrolledWindow(frame, -1, pos, size, style)
+ {
+-	SetBackgroundColour(wxColour("WHITE"));
++	SetBackgroundColour(wxColour(wxT("WHITE")));
+ 	view = v;
+ 	magnification = 1;
+ }
diff --git a/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch b/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch
new file mode 100644
index 000000000000..9d64fabb6a9b
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch
@@ -0,0 +1,73 @@
+--- TreeLib/nodeiterator.h.old	2002-02-24 15:37:17.000000000 -0500
++++ TreeLib/nodeiterator.h	2005-02-27 14:23:30.971981368 -0500
+@@ -128,34 +128,34 @@
+ 
+ template <class N> N *PreorderIterator<N>::begin ()
+ {
+-	cur = root;
+-    return cur;
++	this->cur = this->root;
++    return this->cur;
+ }
+ 
+ template <class N> N *PreorderIterator<N>::next ()
+ {
+-	if (cur->GetChild())
++	if (this->cur->GetChild())
+     {
+-       	stk.push (cur);
+-       	N *p = (N *)(cur->GetChild());
+-        cur = p;
++       	this->stk.push (this->cur);
++       	N *p = (N *)(this->cur->GetChild());
++        this->cur = p;
+     }
+     else
+     {
+-      	while (!stk.empty() && (cur->GetSibling() == NULL))
++      	while (!this->stk.empty() && (this->cur->GetSibling() == NULL))
+         {
+-            cur = stk.top();
+-        	stk.pop();
++            this->cur = this->stk.top();
++        	this->stk.pop();
+         }
+-        if (stk.empty())
+-           	cur = NULL;
++        if (this->stk.empty())
++           	this->cur = NULL;
+         else
+         {
+-        	N *p = (N *)(cur->GetSibling());
+-            cur = p;
++        	N *p = (N *)(this->cur->GetSibling());
++            this->cur = p;
+         }
+     }
+-    return cur;
++    return this->cur;
+ }
+ 
+ 
+--- TreeLib/profile.h.old	2002-12-10 06:37:57.000000000 -0500
++++ TreeLib/profile.h	2005-02-27 14:27:51.205419872 -0500
+@@ -77,7 +77,7 @@
+ 	#include <ctime>
+ #endif    
+ 
+-
++using namespace std;
+ 
+ /**
+  *@typedef std::map <std::string, int, std::less<std::string> > LabelMap;
+--- TreeLib/treedrawer.cpp.old	2003-08-22 06:47:28.000000000 -0400
++++ TreeLib/treedrawer.cpp	2005-02-27 14:26:19.279394752 -0500
+@@ -406,7 +406,7 @@
+         if (q->IsLeaf())
+         {
+             double d = q->GetPathLength() - mMaxPathLength;
+-            mUltrametric = (std::fabs(d) <= 0.0001);
++            mUltrametric = (fabs(d) <= 0.0001);
+ //            cout << mMaxPathLength << ":" << q->GetPathLength() << " " << d << endl;
+         }
+         q = u.next();
diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch
new file mode 100644
index 000000000000..b1c03bbb39f9
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch
@@ -0,0 +1,50 @@
+--- tv.cpp~	2005-10-01 16:47:35.000000000 -0400
++++ tv.cpp	2005-10-01 16:52:30.000000000 -0400
+@@ -312,11 +312,15 @@
+ 	{
+ #ifdef __WXMSW__
+ 		file_menu->AppendSeparator();
+-		file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile");
++		file_menu->Append(SAVEAS_PICTURE_CMD,
++			wxT("Save As Picture...")),
++			wxT("Save picture of tree to metafile");
+ #else
+ 	#ifdef USE_SVG
+ 		file_menu->AppendSeparator();
+-		file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file");
++		file_menu->Append(SAVEAS_PICTURE_CMD,
++			wxT("Save As Picture...")),
++			wxT("Save picture of tree to SVG file");
+ 	#endif
+ #endif
+ 		file_menu->AppendSeparator();
+--- tview.cpp~	2005-10-01 16:47:45.000000000 -0400
++++ tview.cpp	2005-10-01 16:50:42.000000000 -0400
+@@ -184,10 +184,10 @@
+ 	wxString pictureFileName = GetFrame()->GetTitle();
+ 	pictureFileName += wxT(".emf");
+ 	wxFrame *f = GetMainFrame();
+-   	wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
+-        "Enhanced metafile (*.emf)|*.emf",
+-        wxSAVE|wxOVERWRITE_PROMPT);
+-    
++	wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
++		pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"),
++		wxSAVE|wxOVERWRITE_PROMPT);
++
+     if (dialog.ShowModal() == wxID_OK)
+     {
+ 		wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ;
+@@ -204,9 +204,9 @@
+ 	#else
+ 	wxFrame *f = GetMainFrame();
+ 	#endif 
+-    wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName,
+-        "SVG vector picture files (*.svg)|*.svg",
+-        wxSAVE|wxOVERWRITE_PROMPT);
++	wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""),
++		pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"),
++		wxSAVE|wxOVERWRITE_PROMPT);
+ 
+     if (dialog.ShowModal() == wxID_OK)
+     {
diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml
new file mode 100644
index 000000000000..e351ff6c1fa9
--- /dev/null
+++ b/sci-biology/treeviewx/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+		TreeView X is a program for displaying phylogenetic trees on Linux and
+		UNIX platforms. It can read and display NEXUS and Newick format tree
+		files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other
+		programs).
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild
new file mode 100644
index 000000000000..4ff83ca1f34c
--- /dev/null
+++ b/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+WX_GTK_VER="2.8"
+inherit eutils wxwidgets
+
+DESCRIPTION="A phylogenetic tree viewer"
+HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/"
+SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/0.5/tv-${PV}.tar.gz"
+LICENSE="GPL-2"
+
+KEYWORDS="amd64 x86"
+SLOT="0"
+IUSE=""
+
+DEPEND="x11-libs/wxGTK:2.8[X]"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/tv-${PV}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-wxt.patch
+	epatch "${FILESDIR}"/${P}-gcc4.3.patch
+	epatch "${FILESDIR}"/${P}-wx28.patch
+}
+
+src_install() {
+	emake install DESTDIR="${D}" || die "make install failed"
+}