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, 278 insertions, 0 deletions

diff --git a/sci-chemistry/rasmol/Manifest b/sci-chemistry/rasmol/Manifest
new file mode 100644
index 000000000000..7a21a40c5d2b
--- /dev/null
+++ b/sci-chemistry/rasmol/Manifest
@@ -0,0 +1 @@
+DIST rasmol-2.7.5.2-13May11.tar.gz 9768769 SHA256 b975e6e69d5c6b161a81f04840945d2f220ac626245c61bcc6c56181b73a5718 SHA512 c4fd149c002a34d8ce7620a7eed37aa6020acd83fc352a4c16697eb94e6a0377c55455cb6da5fb3f492f879248a6707f677f4b35572f2295b23fc924ddf3128f WHIRLPOOL 261c5351e32a67807d2979b73fbdf83b947aa641568c08fd2f2b0e06115330541a56f7bbd8f05313c86554c321e59cfe11bf5ee613c09249b9e149411c61d5ca
diff --git a/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch
new file mode 100644
index 000000000000..10705165ad47
--- /dev/null
+++ b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch
@@ -0,0 +1,80 @@
+diff --git a/src/Imakefile b/src/Imakefile
+index 03be00e..a0c68f9 100755
+--- a/src/Imakefile
++++ b/src/Imakefile
+@@ -176,7 +176,7 @@ XFORMSLIB_DIR = /usr/local
+ #endif
+ endif
+ XFORMSLIB_INCLUDE_DIR = $(XFORMSLIB_DIR)/include
+-XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib -lforms
++XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib
+ #endif
+ #endif
+ #endif
+@@ -281,17 +281,10 @@ RASMOLDIR = $(USRLIBDIR)/rasmol/
+ 
+ #ifndef USE_XFORMSLIB
+ DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \
+-          -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \
+-          -I$(CQRLIB_INCLUDE_DIR) \
+-          -I$(CVECTOR_INCLUDE_DIR) \
+-          -I$(NEARTREE_INCLUDE_DIR)
++          -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib
+ #else
+ DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \
+-	-D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \
+-	-I$(CQRLIB_INCLUDE_DIR) \
+-	-I$(CVECTOR_INCLUDE_DIR) \
+-	-I$(NEARTREE_INCLUDE_DIR) \
+-  	-I$(XFORMSLIB_INCLUDE_DIR)
++	-D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib
+ #endif
+ 
+ 
+@@ -317,11 +310,11 @@ OBJS = rasmol.o molecule.o abstree.o cmndline.o command.o transfor.o \
+ # Additional RS6000 AIX MITSHM Library
+ # LDLIBS = -lm -lXi -lXextSam $(XLIB)
+ 
+-LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(XFORMSLIB) $(GTKLIBS) \
+-			$(CBFLIB_LDLIB) \
+-			$(CQRLIB_LDLIB) \
+-			$(CVECTOR_LDLIB) \
+-			$(NEARTREE_LDLIB) $(XFORMSLIB_LDLIB)
++LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(GTKLIBS) \
++			-lcbf \
++			-lCQRlib \
++			-lCVector \
++			-lCNearTree -lgfortran
+ 
+ 
+ #
+@@ -425,11 +418,11 @@ $(NEARTREE_DIR):
+ $(NEARTREE_DIR)/CNearTree.c: $(NEARTREE_DIR)
+ #endif		  
+ 
+-$(OBJS):  $(EXTPKGDIR) $(CBFLIB_OBJDEP) \
+-			$(CQRLIB_OBJDEP) \
+-			$(CVECTOR_OBJDEP) \
+-			$(NEARTREE_OBJDEP) \
+-			$(XFORMSLIB_OBJDEP)
++# $(OBJS):  $(EXTPKGDIR) $(CBFLIB_OBJDEP) \
++#			$(CQRLIB_OBJDEP) \
++#			$(CVECTOR_OBJDEP) \
++#			$(NEARTREE_OBJDEP) \
++#			$(XFORMSLIB_OBJDEP)
+ 
+ 
+ gtkwin.c: gtkui.h
+diff --git a/src/Makefile.in b/src/Makefile.in
+index fc6d0af..bad90fc 100755
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -165,7 +165,7 @@ $(CBFLIBDIR)/lib/libcbf.a: $(CBFLIBDIR)
+ 
+ all:		postdownload rasmol rastxt
+ 
+-rasmol:		postdownload $(X11OBJS) $(CBFLIBDIR)/lib/libcbf.a
++rasmol:		postdownload $(X11OBJS) 
+ 		$(CC) -o rasmol $(LFLAGS) $(X11OBJS) $(X11LIBS)
+ 		chmod 755 rasmol
+ 
diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch
new file mode 100644
index 000000000000..22eb229d8a3d
--- /dev/null
+++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch
@@ -0,0 +1,39 @@
+diff -urp RasMol-2.7.5.2/src/command.c RasMol-2.7.5.2_sprintf/src/command.c
+--- RasMol-2.7.5.2/src/command.c	2011-05-15 01:23:49.000000000 +0700
++++ RasMol-2.7.5.2_sprintf/src/command.c	2014-02-12 18:02:24.633489549 +0700
+@@ -1286,7 +1286,7 @@ void ShowRecordCommand( void ) {
+         if (record_on[1]) WriteString("record appearance on\n");
+         else WriteString("record apperance off\n");
+         if (RecordMaxMS == 1.) {
+-            sprintf(param,RecordTemplate);
++            sprintf(param, "%s", RecordTemplate);
+         } else{
+             sprintf(param,RecordTemplate,millisec<0?0:millisec);
+         }
+@@ -1381,7 +1381,7 @@ void ShowPlayCommand( void ) {
+             WriteString(param);
+         }
+         if (PlayMaxMS == 1.) {
+-            sprintf(param,PlayTemplate);
++            sprintf(param, "%s", PlayTemplate);
+         } else{
+             sprintf(param,PlayTemplate,millisec<0?0:millisec);
+         }
+@@ -1469,7 +1469,7 @@ void WriteMovieFrame( void ) {
+         RecordPause = True;
+     } else {
+         if (RecordMaxMS == 1.) {
+-          sprintf(param,RecordTemplate);
++          sprintf(param, "%s", RecordTemplate);
+         } else{
+           sprintf(param,RecordTemplate,millisec);
+         }
+@@ -1505,7 +1505,7 @@ static int PlayMovieFrame( void ) {
+         for (play_frame[1] = 0;play_frame[1]<=millisec; play_frame[1]++) 
+         {
+             if (RecordMaxMS == 1.) {
+-                sprintf(param,PlayTemplate);
++                sprintf(param, "%s", PlayTemplate);
+             } else{
+                 sprintf(param,PlayTemplate,millisec-play_frame[1]);
+             }
diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch
new file mode 100644
index 000000000000..69c19dae5e8d
--- /dev/null
+++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch
@@ -0,0 +1,31 @@
+ src/egg-macros.h           |    3 ++-
+ src/eggfileformatchooser.c |    2 ++
+ 2 files changed, 4 insertions(+), 1 deletions(-)
+
+diff --git a/src/egg-macros.h b/src/egg-macros.h
+index 9a7caad..1a6bce0 100644
+--- a/src/egg-macros.h
++++ b/src/egg-macros.h
+@@ -9,7 +9,8 @@
+ #ifndef _EGG_MACROS_H_
+ #define _EGG_MACROS_H_
+ 
+-#include <glib/gmacros.h>
++#include <glib.h>
++#include <glib/gprintf.h>
+ 
+ G_BEGIN_DECLS
+ 
+diff --git a/src/eggfileformatchooser.c b/src/eggfileformatchooser.c
+index 32ce2ab..febfc2e 100644
+--- a/src/eggfileformatchooser.c
++++ b/src/eggfileformatchooser.c
+@@ -19,6 +19,8 @@
+ #include "eggfileformatchooser.h"
+ #include "egg-macros.h"
+ 
++#include <glib.h>
++#include <glib/gprintf.h>
+ #include <glib/gi18n.h>
+ #include <gtk/gtk.h>
+ #include <string.h>
diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch
new file mode 100644
index 000000000000..3cff0fa2f98f
--- /dev/null
+++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch
@@ -0,0 +1,12 @@
+diff -urp rasmol-2.7.5-23Jul09/src/rasmol.h rasmol-2.7.5-23Jul09-64b/src/rasmol.h
+--- rasmol-2.7.5-23Jul09/src/rasmol.h	2009-07-20 21:08:43.000000000 +0700
++++ rasmol-2.7.5-23Jul09-64b/src/rasmol.h	2013-02-22 14:40:00.378574163 +0700
+@@ -125,6 +125,8 @@
+ #define VECTOR_FAR 
+ #endif
+ 
++#define _LONGLONG
++
+ /*========================*/
+ /*  Default User Options! */
+ /*========================*/
diff --git a/sci-chemistry/rasmol/metadata.xml b/sci-chemistry/rasmol/metadata.xml
new file mode 100644
index 000000000000..b06ec8f7a2fa
--- /dev/null
+++ b/sci-chemistry/rasmol/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <upstream>
+    <remote-id type="sourceforge">openrasmol</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild
new file mode 100644
index 000000000000..642a2641fd59
--- /dev/null
+++ b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild
@@ -0,0 +1,107 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 multilib prefix toolchain-funcs
+
+MY_P="RasMol_${PV}"
+VERS="13May11"
+
+DESCRIPTION="Molecular Graphics Visualisation Tool"
+HOMEPAGE="http://www.openrasmol.org/"
+#SRC_URI="http://www.rasmol.org/software/${MY_P}.tar.gz"
+SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/${P}-${VERS}.tar.gz"
+#SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/RasMol.tar.gz"
+
+LICENSE="|| ( GPL-2 RASLIC )"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-libs/cvector
+	dev-util/gtk-builder-convert
+	>=sci-libs/cbflib-0.9.2
+	>=sci-libs/cqrlib-1.1.2
+	>=sci-libs/neartree-3.1.1
+	x11-libs/cairo
+	x11-libs/gtk+:2
+	x11-libs/libXext
+	x11-libs/libXi
+	x11-libs/vte:0"
+DEPEND="${RDEPEND}
+	app-text/rman
+	x11-misc/imake
+	x11-proto/inputproto
+	x11-proto/xextproto"
+
+#S="${WORKDIR}/${PN}-2.7.5-${VERS}"
+S="${WORKDIR}/RasMol-${PV}"
+
+src_prepare() {
+	cd src || die
+
+	epatch \
+		"${FILESDIR}"/${P}-glib.h.patch \
+		"${FILESDIR}"/${P}-format-security.patch \
+		"${FILESDIR}"/${P}-longlong.patch
+
+	if use amd64 || use amd64-linux; then
+		mv rasmol.h rasmol_amd64_save.h && \
+		echo "#define _LONGLONG"|cat - rasmol_amd64_save.h > rasmol.h
+	fi
+
+	sed \
+		-e 's:-traditional::g' \
+		-i Makefile* || die
+
+	cat > Imakefile <<- EOF
+	#define PIXELDEPTH 32
+	#define GTKWIN
+	EOF
+
+	cat Imakefile_base >> Imakefile || die
+	epatch "${FILESDIR}"/2.7.5-bundled-lib.patch
+
+	eprefixify Imakefile
+
+	sed \
+		-e 's:vector.c:v_ector.c:g' \
+		-e 's:vector.o:v_ector.o:g' \
+		-e 's:vector.h:v_ector.h:g' \
+		-i *akefile* || die
+
+	sed \
+		-e 's:vector.h:v_ector.h:g' \
+		-i *.c *.h || die
+
+	mv vector.c v_ector.c || die
+	mv vector.h v_ector.h || die
+
+	xmkmf -DGTKWIN || die "xmkmf failed with ${myconf}"
+}
+
+src_compile() {
+	emake -C src clean
+	emake \
+		-C src \
+		DEPTHDEF=-DTHIRTYTWOBIT \
+		CC="$(tc-getCC)" \
+		CDEBUGFLAGS="${CFLAGS}" \
+		EXTRA_LDOPTIONS="${LDFLAGS}"
+}
+
+src_install () {
+	libdir=$(get_libdir)
+	insinto /usr/${libdir}/${PN}
+	doins doc/rasmol.hlp
+	dobin src/rasmol
+	dodoc PROJECTS {README,TODO}.txt doc/*.{ps,pdf}.gz doc/rasmol.txt.gz
+	doman doc/rasmol.1
+	insinto /usr/${libdir}/${PN}/databases
+	doins data/*
+
+	dohtml -r *html doc/*.html html_graphics
+}