reinit the tree, so we can have metadata

7 files changed, 288 insertions, 0 deletions

diff --git a/sci-chemistry/rasmol/Manifest b/sci-chemistry/rasmol/Manifest
new file mode 100644
index 000000000000..5672f0f3675c
--- /dev/null
+++ b/sci-chemistry/rasmol/Manifest
@@ -0,0 +1,9 @@
+AUX 2.7.5-bundled-lib.patch 2513 SHA256 86fc627ae39fbc6d85063436b1e05e19745fd4690e6df70fd6111f99c1b90505 SHA512 940e85bbe35ed6055d8deb1d761e925aec3b60d63c3e91bcc3c08596f1b8269efd4c8a257ff9efdbe32888e987852e85ed19cba5566d8d610e8d625a23b0994a WHIRLPOOL ffbe6399b1176601459dafb8bed6267fbff60d859761a7e0ecbf55b4b0c2f607888a11c0ca9c66278e3cc514ed2b44b769cac3af8099a10efd8decd7bac37077
+AUX rasmol-2.7.5.2-format-security.patch 1617 SHA256 6171a944ac63bcbc18e8d4a1aabb03dca5297cedad00eef8a38cb78253f8c3c8 SHA512 cab29465d5830e669eca152880ae60c403f90668ee5bf97e3694b6e754e2e23086a520717c2df990c74fcfbafc761a460bea111d868a57ae63f13bce1603f074 WHIRLPOOL dcf0437e73150f0dc7ad5c7876a28d74e9d1df51033f6d9bb089876895dde97871b0f2e48bc2daa75cd35f9a5e2739df33d089e5fe556b238c8f7d64d4b4c42e
+AUX rasmol-2.7.5.2-glib.h.patch 770 SHA256 4093621678676bdc7c517f6d6c260f495b9d946d57691d8e58371b627cd6c178 SHA512 d743b89817d0ed2aa551f3a6529e5bcc50c811d79c0deddd50d07a59614cb0c2d71500452ff9aec4b4b84e4985d9851f61aafa30196356aa1724212b5159375e WHIRLPOOL 250e59fbafe5d53f1dfd77bc2392cf085b07968578675e61635c8ca2e5de1dd60f060240f2a9afdb088285bac3a94cb695cecd3abbb93214f2d6fcf584fe8a16
+AUX rasmol-2.7.5.2-longlong.patch 396 SHA256 98503ec652d13e62443275536d86a8abefae6f6006441425026d400f40f25607 SHA512 4c3ce01ade36fe8a9512bdac62bcd47268bcc5a0448f4af69b26d8add9cc8495d376bac33a8ae5aeae42fa114a1cba980ce86559bf2d52334257f2e001c011d3 WHIRLPOOL 812ff6f3b2d3a6d5dc4ce1c0a9ebf627998b4df355bf435ff1a2e43b3ba369d29fed8cd8ffeef472a62735f71a4bfa2bf89812dafb7f11ec4be34716793f95a7
+DIST rasmol-2.7.5.2-13May11.tar.gz 9768769 SHA256 b975e6e69d5c6b161a81f04840945d2f220ac626245c61bcc6c56181b73a5718 SHA512 c4fd149c002a34d8ce7620a7eed37aa6020acd83fc352a4c16697eb94e6a0377c55455cb6da5fb3f492f879248a6707f677f4b35572f2295b23fc924ddf3128f WHIRLPOOL 261c5351e32a67807d2979b73fbdf83b947aa641568c08fd2f2b0e06115330541a56f7bbd8f05313c86554c321e59cfe11bf5ee613c09249b9e149411c61d5ca
+EBUILD rasmol-2.7.5.2-r2.ebuild 2299 SHA256 736f1d571389b382043a3562397e04ce95fb9306b6dc6783cae826ad5abbafc2 SHA512 c725dde02ff311e385373f6125f254ff9ba3ab7e59164315edcfb852f587495fc1ca30e48a65eaad4c9756ba95c682100034808e8fbbc2a97de4f5c954f82e02 WHIRLPOOL d6571bbdebd614d6777d3405f9ceab7fb6fb9edf9ff8ea150a8946a7c40126270d1f10aad21d7779c933a178e07603227d8e4cbc9203b454563e8f1a0072456a
+MISC ChangeLog 2594 SHA256 6e7e7df4aec74262f9a00545174147af18ee6e2b7ae0e41f1f8e13f35aecaa83 SHA512 930f250703285b0efc579ec45f71a2f1659cba72265788dcaf2fbd042b2c162c43916cfd215c2a853a5cacc61f3e8fb9b6de90045ff2c08e48fe39889de09105 WHIRLPOOL 56c528196574bb8002ad3947c48c43bc0331960d49d5cd0b58093c95ac770dbf7ab5c2a16513178fd8221fad541662896c12c9cf5c77c3056fe54e3a20f36da1
+MISC ChangeLog-2015 8025 SHA256 04c9b2b53016b1f3704e7b3b3c20149411a861054d16ab985b8b1df77ef0abe8 SHA512 1b38bdbd882c910e5127c2bbffd337c485415c82dea0f6208742b691e016ec6f058f8dcc0151cda4939527bf835cde83b105885a19c744ffe39a463f9f1d0439 WHIRLPOOL fe46f78161c4ef1637db917689a30f8ed0b4c934ec7c3d071d4305e03088fa387fd6d3e9f2565a16db659b70c96c8931ad60391a148bef8b0e46a8eafd864fd0
+MISC metadata.xml 355 SHA256 76c1dff8297a72d84445be9ede0d498e9bc76cb1c240da8cfeb2ae5ba394b645 SHA512 98822367149551ef6af6d75e4bd0b9104f1a625a5a17e1a2dad32e7ed83345870dc45392525cfe7e49514eae29f986e8ac2ed253ec22fec94d6152f96620b916 WHIRLPOOL d43bf1f6f203a892e4e3630d2101be9363c0dc970f4714678f9c53d99f94e95b6de5350cfc650e9c254bcaf4cba08bef04436764b5c3c26804c6eedfda3881c0
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..59ea086025a2
--- /dev/null
+++ b/sci-chemistry/rasmol/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <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..3335b5ae5a47
--- /dev/null
+++ b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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${PN}/RasMol/RasMol_2.7.5/RasMol.tar.gz"
+
+LICENSE="|| ( GPL-2 RASLIC )"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-libs/cvector
+	dev-util/gtk-builder-convert
+	>=sci-libs/cbflib-0.9.2
+	>=sci-libs/cqrlib-1.1.2
+	>=sci-libs/neartree-3.1.1
+	x11-libs/cairo
+	x11-libs/gtk+:2
+	x11-libs/libXext
+	x11-libs/libXi
+	x11-libs/vte:0"
+DEPEND="${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
+}