reinit the tree, so we can have metadata

9 files changed, 303 insertions, 0 deletions

diff --git a/sci-visualization/ggobi/Manifest b/sci-visualization/ggobi/Manifest
new file mode 100644
index 000000000000..71e4cf527d97
--- /dev/null
+++ b/sci-visualization/ggobi/Manifest
@@ -0,0 +1,12 @@
+AUX ggobi-2.1.10-desktop.patch 394 SHA256 cf928b6b9df622466d68723c5d26120e2d1203b1ed1a68cdd7b516e354ddab24 SHA512 db54bb75d8a56a51e3731f6f01cb1a8986aa8fc70a5959ac9ebbb604e55b6367f7bcd48837c09f3e933c1e20bd5b6901007285976cd2b93999a277613e3b3065 WHIRLPOOL 15009c5b22c55e4359734375a5f12242fcad55a3d5c44c1cdf1f8046a7d988fd85f27144dc02202d6e6e6576a8f0555c30420e29e7bb48c59ebc71e4e3c9abe3
+AUX ggobi-2.1.10-hardened.patch 1912 SHA256 1e525e65e66edd947ccabce1e5c9f7a3e1728227b3009481a66596ec50dacdc7 SHA512 069f0dc1594d2616dccc7fec5ea89f2f31b0e3368471f4163071e4afb70f58dfad62afee85536b95b03ec15613a6261e736f2d6d97448d2ee08976f10abe8e73 WHIRLPOOL 23cb3295c3b57200dec4a161c43249654d5cfeb70cf791de0e9447b5168ed6e1d50f651baea5126d8eb9762de8ff4c70e7c54799215693b851c209e0bea128db
+AUX ggobi-2.1.11-Wformat-security.patch 1109 SHA256 07a4649bbbb085911142a33a2fa7de56ee038431f840fb8480d425c51a09049f SHA512 18162cc1ab6e8065de5602b54058f4ee11f9cb25d8ab0ed3bc176802687009f9d75c7c3a9909cd3439544c8989de0d53e3bd9744183f44fc07e8b6ba456200e5 WHIRLPOOL afda6fcf2d2ed1f4c9bbc431437843c6a8d83d57fac0ca97c0837ee063f285f02c948210ce656f833ea0f117979aefd8189e057a2d9b89f541db2ceb2125b0d1
+AUX ggobi-2.1.8-plugindir.patch 499 SHA256 201af2941a8dedbc42fb42d9f6cc549853d5655d08be6b6611009e9c7512c365 SHA512 07108552ac0bda21fec8b7aa83e25a51abd1fcc6630347d1e1348b467a0d246c91f6400d148b6781961a8e38eb31a0c96a86de0df48984a351c072f950d2be11 WHIRLPOOL f313f54e4d4aa8f81895713bd246d246f02500f792e40ac0381d456dde61d91d6ac0e95f2489e1294410513bdddb728485dba0e157bf908182b8ca962d402c2d
+AUX ggobi-2.1.9-as-needed.patch 1716 SHA256 748a07ee90af08b056bc1dbd5b511e774245d5f1e62af234f21ed98192a26ac1 SHA512 6e96f461e71630b68ba0ecc48fa94f8b7ab211cd26c95b91d65604a23c3fa13b20316e90397f857857c21cd8ddc6a8f67efcc7ec62a8d2c48c349b532aad8797 WHIRLPOOL e50ab89c823f210b4333ef8ed95ac01fec8e5ea26debffc2b6bd5eafcc97f87181c59f8063e198a820c4081b9f00521337cf5dc33d0329f521ca65d36d16a657
+DIST ggobi_2.1.10.orig.tar.bz2 2776784 SHA256 08881aacb70a7a80e3778197bb4c673e634aea403fb7f9e282df189764b96aa3 SHA512 40bc4a7fae992bf327d6b36c5aea7802279a3b6229242f31386e771636b4561260914a7fefb6a6337c1e1ab5a0682fbdd626389b83d9b57d0c2d050fac3723e5 WHIRLPOOL ee751f5278937433db76b8c43d032e1dd7d78541848ab7da412a2da2bebb9300bb4689578b1809328368024f5691b3371b579c882ea01f4ee37ae521cb23e76f
+DIST ggobi_2.1.11.orig.tar.bz2 2787709 SHA256 2c4ddc3ab71877ba184523e47b0637526e6f3701bd9afb6472e6dfc25646aed7 SHA512 d34c6569d05d1e680101b62745012940c1e18c1588cd37b89b26b89e9eed9bab8fc53e0585a595b6cb4c9f2bb7d603ca4252cb6a6ba344bbc24e5cc5fd8a6dc1 WHIRLPOOL 9e686287fdb41f840c45b9ab92c184a0d624eb86a93233e4934cebd0e550ac25fe5ae3b06f6c95ebf1098efbd6062b9c9161ffbb26b3e3a43833443536af4987
+EBUILD ggobi-2.1.10.ebuild 1346 SHA256 d558b47ab75416f9d8d18d6a97410c3ebbd428b512b2c12f4899e65d50018e8d SHA512 e2c29578b022c2e67d29646c6f86bfb0607a202bec21125dcee83aa24eacce30e7fb78a09c1677ed2db2466dd47113eb5adb017ae7d49e0108b8adffec6c04a9 WHIRLPOOL f590b7da600843daaf25e72cc38fdb38748836d4420da2361eb27ab0d29ba532e0da5ac7106e428cecac173d73508811d036944b79f8be01220a277e2fcc8198
+EBUILD ggobi-2.1.11.ebuild 1352 SHA256 fcf0421ef4278f7321236a68f0b5deb0f9250321e970cc49093c6ac7d7d32017 SHA512 86a85a0eae27df877ac1fc5f07467a16655dd1d8132be7176bf5a62f1ac2a0afc2aede72e22432bbf17389699c4e91b930130075be1f481e9f2ca7e4f1c491f9 WHIRLPOOL f1ca377600ad1ac7b06d8b8b8f48f515ae75c6659f9e363ad180b17192444717921352fdcfa66d2ea6103c40317fdb44d2dd8c1f7e7e3e4a425aed754d1f481b
+MISC ChangeLog 3674 SHA256 0a1569d5c77f71dda1952bb4d6c2782841f97e51121fa3f8a95b5d01f3228693 SHA512 8bcd3616d28a95825b6648b8d80e9211fc96dc22773d9d83187c8f3b0bdede51c80c34a10038472d3009b3b5d0b72d450dfc3493626456e4e1681947a26cefa5 WHIRLPOOL 0a295f6301de053f60a3d0bbd7ebee31a242401dfe0894553715957001f2aada5eebfed09399f71e3ad28a923ae6adc34f5942ea78ff310037d548d624db5eed
+MISC ChangeLog-2015 2561 SHA256 9e783c810240085c2e18c8993485f2738bf32ec613b606113a5a0f6eb1115f80 SHA512 115ec2fcef7af8d419ded30a09e9527a0479c7a3e1f6a3e1127e1b833f2a015d6f41d1b06df7d80e50f630c335c3a27e2c456a46ec995fd409a58076efe31050 WHIRLPOOL 90a5013a10fb2eeb07ad5f55dbc37089404de63c36a15e7380491e55a86d302b21e1721b1ec7e0befc9b813c1e93fb54dcb7b6235a09a9258e03464f1c61031c
+MISC metadata.xml 622 SHA256 86d81c7fea11d5be891f744c2362dcd1475dfc21d9be84fba7314afd30d888ca SHA512 3ffd9440d573a564db639a4f992fdda62c5f20a9e9d8f28126e4ac8e1e4958e543fea8315a3b1e10773d6d119046154d98d248e9b68a852233c5d0c90c141ab0 WHIRLPOOL 06c1530689d54a560d5e8da05da12d3da7458a035a03e4ac4b4e6207ed5b3b238c03f9367ef78ccae4116f5a8f496ab9cf7e90329a365a157c643e414a4b8ed4
diff --git a/sci-visualization/ggobi/files/ggobi-2.1.10-desktop.patch b/sci-visualization/ggobi/files/ggobi-2.1.10-desktop.patch
new file mode 100644
index 000000000000..388cb85c975c
--- /dev/null
+++ b/sci-visualization/ggobi/files/ggobi-2.1.10-desktop.patch
@@ -0,0 +1,11 @@
+--- xdg/ggobi.desktop.orig	2013-02-24 22:20:02.616872402 -0800
++++ xdg/ggobi.desktop	2013-02-24 22:20:13.293924862 -0800
+@@ -6,6 +6,6 @@
+ Comment=Multivariate interactive graphics for exploratory data analysis
+ TryExec=ggobi
+ Exec=ggobi
+-Icon=ggobi.png
+-Categories=Graphics;2DGraphics
++Icon=ggobi
++Categories=Graphics;2DGraphics;
+ MimeType=text/comma-separated-values;text/csv;application/csv;
diff --git a/sci-visualization/ggobi/files/ggobi-2.1.10-hardened.patch b/sci-visualization/ggobi/files/ggobi-2.1.10-hardened.patch
new file mode 100644
index 000000000000..63681a0a03ea
--- /dev/null
+++ b/sci-visualization/ggobi/files/ggobi-2.1.10-hardened.patch
@@ -0,0 +1,66 @@
+Description: Upstream changes introduced in version 2.1.10-4
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ ggobi (2.1.10-4) unstable; urgency=low
+ .
+   * src/ggobi.c: Applied patch kindly supplied by Michael Lawrence to
+     address issues found under hardened compiler flags (Closes: #646260)
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Dirk Eddelbuettel <edd@debian.org>
+Bug-Debian: http://bugs.debian.org/646260
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- ggobi-2.1.10.orig/src/ggobi.c
++++ ggobi-2.1.10/src/ggobi.c
+@@ -698,10 +698,10 @@ ValidateGGobiRef (ggobid * gg, gboolean
+   }
+ 
+   if (fatal) {
+-    g_error (error_msg);
++    g_error ("%s", error_msg);
+   }
+   else
+-    g_critical (error_msg);
++    g_critical ("%s", error_msg);
+ 
+   return (NULL);
+ }
+@@ -718,9 +718,9 @@ ValidateDatadRef (GGobiData * d, ggobid
+   }
+ 
+   if (fatal)
+-    g_error (error_msg);
++    g_error ("%s", error_msg);
+   else
+-    g_critical (error_msg);
++    g_critical ("%s", error_msg);
+ 
+   return (NULL);
+ }
+@@ -739,9 +739,9 @@ ValidateDisplayRef (displayd * d, ggobid
+   }
+ 
+   if (fatal)
+-    g_error (error_msg);
++    g_error ("%s", error_msg);
+   else
+-    g_critical (error_msg);
++    g_critical ("%s", error_msg);
+ 
+   return (NULL);
+ }
diff --git a/sci-visualization/ggobi/files/ggobi-2.1.11-Wformat-security.patch b/sci-visualization/ggobi/files/ggobi-2.1.11-Wformat-security.patch
new file mode 100644
index 000000000000..960d940a7908
--- /dev/null
+++ b/sci-visualization/ggobi/files/ggobi-2.1.11-Wformat-security.patch
@@ -0,0 +1,36 @@
+Fix -Wformat -Werror=format-security errors caused by wrong fprintf calls
+See also: https://bugs.gentoo.org/show_bug.cgi?id=577430
+* utils_ui.c: In function ‘quick_message’:
+* utils_ui.c:192:29: error: format not a string literal and no format arguments [-Werror=format-security]
+*                              message);
+
+--- ggobi-2.1.11/src/utils_ui.c
++++ ggobi-2.1.11/src/utils_ui.c
+@@ -189,7 +189,7 @@
+ 
+   dialog =
+     gtk_message_dialog_new (NULL, 0, GTK_MESSAGE_INFO, GTK_BUTTONS_OK,
+-                            message);
++                            "%s", message);
+ 
+   if (modal)
+     gtk_window_set_modal (GTK_WINDOW (dialog), true);
+--- ggobi-2.1.11/src/write_xml.c
++++ ggobi-2.1.11/src/write_xml.c
+@@ -37,14 +37,14 @@
+ write_xml_string(FILE *f, gchar *str)
+ {
+   gchar *fmtstr = g_markup_printf_escaped("%s", str);
+-  fprintf(f, fmtstr);
++  fprintf(f, "%s", fmtstr);
+   g_free(fmtstr);
+ }
+ static void
+ write_xml_string_fmt(FILE *f, gchar *fmt, gchar *str)
+ {
+   gchar *fmtstr = g_markup_printf_escaped(fmt, str);
+-  fprintf(f, fmtstr);
++  fprintf(f, "%s", fmtstr);
+   g_free(fmtstr);
+ }
+ 
diff --git a/sci-visualization/ggobi/files/ggobi-2.1.8-plugindir.patch b/sci-visualization/ggobi/files/ggobi-2.1.8-plugindir.patch
new file mode 100644
index 000000000000..0476f47a816d
--- /dev/null
+++ b/sci-visualization/ggobi/files/ggobi-2.1.8-plugindir.patch
@@ -0,0 +1,11 @@
+--- plugins/Makefile.plugin.orig	2009-12-14 22:15:01.000000000 +0000
++++ plugins/Makefile.plugin	2009-12-14 22:15:16.000000000 +0000
+@@ -2,7 +2,7 @@
+ 
+ # Every plugin provides a single library to GGobi, define it here.
+ # Its name should start with 'lib' and end with '.la'.
+-plugindir = $(datadir)/ggobi/plugins/$(PACKAGE_NAME)
++plugindir = $(libdir)/ggobi/plugins/$(PACKAGE_NAME)
+ plugin_LTLIBRARIES        = plugin.la
+ 
+ # Most plugins will only require GGobi and its dependencies (gtk, libxml2)
diff --git a/sci-visualization/ggobi/files/ggobi-2.1.9-as-needed.patch b/sci-visualization/ggobi/files/ggobi-2.1.9-as-needed.patch
new file mode 100644
index 000000000000..3bec9b55c21d
--- /dev/null
+++ b/sci-visualization/ggobi/files/ggobi-2.1.9-as-needed.patch
@@ -0,0 +1,40 @@
+--- configure.ac.orig	2012-06-26 05:46:07.000000000 +0100
++++ configure.ac	2012-06-26 05:46:44.000000000 +0100
+@@ -178,6 +178,8 @@
+  echo "Looking for gtk2"
+ 
+ PKG_CHECK_MODULES(GTK, [gtk+-2.0 >= 2.6.0])
++AC_CHECK_LIB(m,sqrt)
++PKG_CHECK_MODULES(GMODULE, [gmodule-2.0 >= 2.0])
+ 
+ AC_SUBST(GTK_CFLAGS)
+ AC_SUBST(GTK_LIBS)
+
+--- src/Makefile.am.orig	2012-06-26 04:53:20.000000000 +0100
++++ src/Makefile.am	2012-06-26 04:54:04.000000000 +0100
+@@ -4,7 +4,6 @@
+ libggobi_la_GOBHEADERS = $(libggobi_la_GOBS:%.gob=ggobi-%.h)
+ libggobi_la_GOBOBJECTS = $(libggobi_la_GOBS:%.gob=ggobi-%.lo)
+ libggobi_la_GOBSTAMPS = $(libggobi_la_GOBS:%.gob=.%.gob.stamp)
+-libggobi_la_LDFLAGS  = @GTK_LIBS@ @LIBXML_LIBS@
+ libggobi_la_BUILT = array.c ash1d.c barchart.c barchartClass.c \
+   barchart_ui.c brush.c brush_api.c brush_bins.c brush_init.c brush_link.c \
+   brush_ui.c color.c color_ui.c cpanel.c display.c display_tree.c display_ui.c \
+@@ -27,7 +26,7 @@
+   write_csv.c write_xml.c wvis.c wvis_ui.c xlines.c xyplot.c \
+   xyplot_ui.c $(libggobi_la_GOBSOURCES)
+ libggobi_la_SOURCES = $(libggobi_la_BUILT) $(libggobi_la_GOBSTAMPS)
+-libggobi_la_LIBADD = $(libggobi_la_GOBOBJECTS)
++libggobi_la_LIBADD = $(libggobi_la_GOBOBJECTS) @GTK_LIBS@ @LIBXML_LIBS@ @GMODULE_LIBS@
+ libggobi_la_DEPENDENCIES = $(libggobi_la_GOBOBJECTS)
+ pkginclude_HEADERS = GGobiAPI.h ggobiClass.h tour1d_pp.h GGobiApp.h \
+   noop-toggle.h tour2d_pp.h GGobiEvents.h parcoordsClass.h tour_pp.h \
+@@ -59,7 +58,7 @@
+ # Windows specific
+ if OS_WIN32
+ libggobi_la_DEPENDENCIES+=libggobi.def
+-libggobi_la_LDFLAGS+=-Wc,-s -no-undefined -export-symbols libggobi.def
++libggobi_la_LDFLAGS=-Wc,-s -no-undefined -export-symbols libggobi.def
+ ggobi_LDFLAGS = -mwindows -s
+ endif
+ 
diff --git a/sci-visualization/ggobi/ggobi-2.1.10.ebuild b/sci-visualization/ggobi/ggobi-2.1.10.ebuild
new file mode 100644
index 000000000000..79dd49b4198b
--- /dev/null
+++ b/sci-visualization/ggobi/ggobi-2.1.10.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+inherit eutils autotools
+
+DESCRIPTION="Visualization program for exploring high-dimensional data"
+HOMEPAGE="http://www.ggobi.org/"
+# source code release is not well published
+#SRC_URI="http://www.ggobi.org/downloads/${P}.tar.bz2"
+SRC_URI="mirror://debian/pool/main/g/${PN}/${PN}_${PV}.orig.tar.bz2"
+
+LICENSE="CPL-1.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc minimal nls"
+
+RDEPEND="
+	dev-libs/libxml2:2
+	media-gfx/graphviz
+	x11-libs/gtk+:2"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	sed -i \
+		-e 's|ND_coord_i|ND_coord|' \
+		plugins/GraphLayout/graphviz.c || die
+	rm m4/libtool.m4 m4/lt*m4 plugins/*/aclocal.m4 || die
+	epatch \
+		"${FILESDIR}"/${PN}-2.1.8-plugindir.patch \
+		"${FILESDIR}"/${PN}-2.1.9-as-needed.patch \
+		"${FILESDIR}"/${PN}-2.1.10-hardened.patch \
+		"${FILESDIR}"/${PN}-2.1.10-desktop.patch
+	# need the ${S} for recursivity lookup
+	AT_M4DIR="${S}"/m4 eautoreconf
+}
+
+src_configure() {
+	econf \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		--disable-rpath \
+		$(use_enable nls) \
+		$(use_with !minimal all-plugins)
+}
+
+src_compile() {
+	emake all ggobirc
+}
+
+src_install() {
+	default
+	insinto /etc/xdg/ggobi
+	doins ggobirc
+	use doc || rm "${ED}"/usr/share/doc/${PF}/*.pdf
+}
diff --git a/sci-visualization/ggobi/ggobi-2.1.11.ebuild b/sci-visualization/ggobi/ggobi-2.1.11.ebuild
new file mode 100644
index 000000000000..658728197cf2
--- /dev/null
+++ b/sci-visualization/ggobi/ggobi-2.1.11.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+inherit eutils autotools
+
+DESCRIPTION="Visualization program for exploring high-dimensional data"
+HOMEPAGE="http://www.ggobi.org/"
+# source code release is not well published
+#SRC_URI="http://www.ggobi.org/downloads/${P}.tar.bz2"
+SRC_URI="mirror://debian/pool/main/g/${PN}/${PN}_${PV}.orig.tar.bz2"
+
+LICENSE="CPL-1.0"
+SLOT="0"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE="doc minimal nls"
+
+RDEPEND="
+	dev-libs/libxml2:2
+	media-gfx/graphviz
+	x11-libs/gtk+:2"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	sed -i \
+		-e 's|ND_coord_i|ND_coord|' \
+		plugins/GraphLayout/graphviz.c || die
+	rm m4/libtool.m4 m4/lt*m4 plugins/*/aclocal.m4 || die
+	epatch \
+		"${FILESDIR}"/${PN}-2.1.8-plugindir.patch \
+		"${FILESDIR}"/${PN}-2.1.9-as-needed.patch \
+		"${FILESDIR}"/${PN}-2.1.10-desktop.patch \
+		"${FILESDIR}"/${PN}-2.1.11-Wformat-security.patch
+	# need the ${S} for recursivity lookup
+	AT_M4DIR="${S}"/m4 eautoreconf
+}
+
+src_configure() {
+	econf \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		--disable-rpath \
+		$(use_enable nls) \
+		$(use_with !minimal all-plugins)
+}
+
+src_compile() {
+	emake all ggobirc
+}
+
+src_install() {
+	default
+	insinto /etc/xdg/ggobi
+	doins ggobirc
+	use doc || rm "${ED}"/usr/share/doc/${PF}/*.pdf
+}
diff --git a/sci-visualization/ggobi/metadata.xml b/sci-visualization/ggobi/metadata.xml
new file mode 100644
index 000000000000..a0223eece275
--- /dev/null
+++ b/sci-visualization/ggobi/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>sci@gentoo.org</email>
+	<name>Gentoo Science Project</name>
+</maintainer>
+<longdescription lang="en">
+  GGobi is an open source visualization program for exploring
+  high-dimensional data. It provides highly dynamic and interactive
+  graphics such as tours, as well as familiar graphics such as the
+  scatterplot, barchart and parallel coordinates plots. Plots are
+  interactive and linked with brushing and identification.    
+</longdescription>
+</pkgmetadata>