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, 163 insertions, 0 deletions

diff --git a/sci-chemistry/probe/Manifest b/sci-chemistry/probe/Manifest
new file mode 100644
index 000000000000..f5dd9226d404
--- /dev/null
+++ b/sci-chemistry/probe/Manifest
@@ -0,0 +1,2 @@
+DIST probe.2.12.110413.src.zip 262460 SHA256 90cd0a693683958a8ac05d13a47c2b464f2939df24369bf5c568f59913756de4 SHA512 ac6a92f1666d1819c0dede5ea97113c9e03271c42b829d88a2b65041dec7f853441fc61e94e48782078884a9a69c1043432ca3576768d31bfe9190d3ea1da4c8 WHIRLPOOL f6e6ec43016d14114ae5cbfdbfd1cdb5bdf0c6a1c34742b0fef0cfe5ee39409a41b4b2127fbefe526d66d99c33b91ef5e3ea4c9de33784f9ea493700e8bc8784
+DIST probe.2.13.110909.src.zip 131063 SHA256 df14b76d27a7c43b2b57c315d0ad71cdf6acc7943c43195a797162be7816fa71 SHA512 5efa066873d0e139da66bf8edb541fe42df94e99cab171ad8d06a8a6f5caada982ef5b18481e748b224dbed86f63c99237d04ecd107c82855b44de91fb6d2b16 WHIRLPOOL 12f6fefe1b03b71268f39fa3aa7ad796230c76c2e029b8dc86955abd43c8e3f09f7591f84cd79c7ba11037d5b323c922ddf36abf6911d556981f5cc21378912f
diff --git a/sci-chemistry/probe/files/2.12.110413-as-needed.patch b/sci-chemistry/probe/files/2.12.110413-as-needed.patch
new file mode 100644
index 000000000000..95368625505d
--- /dev/null
+++ b/sci-chemistry/probe/files/2.12.110413-as-needed.patch
@@ -0,0 +1,38 @@
+ Makefile |   13 ++++++-------
+ 1 files changed, 6 insertions(+), 7 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e6a740e..8f74d6a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,14 +1,12 @@
+-MACHINEFLAGS = 
+-CFLAGS = $(MACHINEFLAGS)
+-LFLAGS = -lm $(MACHINEFLAGS)
++LIBS = -lm
+ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
+-	 parse.o atomprops.o stdconntable.o autobondrot.o
++	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
+ 
+ .c.o:
+-	cc -c $*.c $(CFLAGS)
++	$(CC) $(CFLAGS) -c $*.c
+ 
+ probe: probe.o $(OBJLIST)
+-	cc -o $@ probe.o $(OBJLIST) $(LFLAGS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ probe.o $(OBJLIST) $(LIBS)
+ 
+ clean:
+ 	@rm -f *.o *.ckp
+@@ -30,9 +28,10 @@ parse.o:	./parse.h	./utility.h	parse.c
+ probe.o:	./abin.h	./atomprops.h	./autobondrot.h	./dots.h	./geom3d.h \
+ 		./parse.h	./probe.h	./readPDBrecs.h	./select.h \
+ 		./stdconntable.h	./utility.h	probe.c
+-readPDBrecs.o:	./geom3d.h	./readPDBrecs.h	./utility.h	readPDBrecs.c
++readPDBrecs.o:	./geom3d.h	./readPDBrecs.h	./utility.h	./hybrid_36_c.h readPDBrecs.c
+ select.o:	./abin.h	./atomprops.h	./geom3d.h	./parse.h	./select.h \
+ 		./stdconntable.h	./utility.h	select.c
+ stdconntable.o:	./stdconntable.h	stdconntable.c
+ utility.o:	utility.c
++hybrid_36_c.o:  ./hybrid_36_c.h	hybrid_36_c.c
+ # DO NOT DELETE THIS 2nd LINE -- make depend uses it
diff --git a/sci-chemistry/probe/files/as-needed.patch b/sci-chemistry/probe/files/as-needed.patch
new file mode 100644
index 000000000000..9ddecf5f569e
--- /dev/null
+++ b/sci-chemistry/probe/files/as-needed.patch
@@ -0,0 +1,21 @@
+diff --git a/Makefile b/Makefile
+index 68d7469..bcb821c 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,6 @@
+ MACHINEFLAGS = 
+ CFLAGS = $(MACHINEFLAGS)
+-LFLAGS = -lm $(MACHINEFLAGS)
++LFLAGS = -lm
+ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
+ 	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
+ 
+@@ -8,7 +8,7 @@ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
+ 	cc -c $*.c $(CFLAGS)
+ 
+ probe: probe.o $(OBJLIST)
+-	cc -o $@ probe.o $(OBJLIST) $(LFLAGS)
++	cc $(MACHINEFLAGS) -o $@ probe.o $(OBJLIST) $(LFLAGS)
+ 
+ clean:
+ 	@rm -f *.o *.ckp
diff --git a/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch
new file mode 100644
index 000000000000..df7040c3ba1d
--- /dev/null
+++ b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch
@@ -0,0 +1,25 @@
+ Makefile |    8 +++-----
+ 1 files changed, 3 insertions(+), 5 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 9031bd0..8f74d6a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,14 +1,12 @@
+-MACHINEFLAGS = 
+-CFLAGS = $(MACHINEFLAGS)
+-LFLAGS = -static -lm $(MACHINEFLAGS)
++LIBS = -lm
+ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
+ 	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
+ 
+ .c.o:
+-	cc -c $*.c $(CFLAGS)
++	$(CC) $(CFLAGS) -c $*.c
+ 
+ probe: probe.o $(OBJLIST)
+-	cc -o $@ probe.o $(OBJLIST) $(LFLAGS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ probe.o $(OBJLIST) $(LIBS)
+ 
+ clean:
+ 	@rm -f *.o *.ckp
diff --git a/sci-chemistry/probe/metadata.xml b/sci-chemistry/probe/metadata.xml
new file mode 100644
index 000000000000..e42d0af60f42
--- /dev/null
+++ b/sci-chemistry/probe/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/probe/probe-2.12.110413.ebuild b/sci-chemistry/probe/probe-2.12.110413.ebuild
new file mode 100644
index 000000000000..bb0a36a232de
--- /dev/null
+++ b/sci-chemistry/probe/probe-2.12.110413.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}"
+
+DESCRIPTION="Evaluates atomic packing within or between molecules"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip"
+
+SLOT="0"
+LICENSE="richardson"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}"/trunk
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-as-needed.patch
+	# Respect CC
+	sed -i \
+		-e 's:cc:$(CC):g' \
+		"${S}"/Makefile || die
+	tc-export CC
+}
+
+src_install() {
+	dobin "${S}"/probe
+	dodoc "${S}"/README*
+}
diff --git a/sci-chemistry/probe/probe-2.13.110909.ebuild b/sci-chemistry/probe/probe-2.13.110909.ebuild
new file mode 100644
index 000000000000..a841b16de30f
--- /dev/null
+++ b/sci-chemistry/probe/probe-2.13.110909.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}"
+
+DESCRIPTION="Evaluates atomic packing within or between molecules"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip"
+
+SLOT="0"
+LICENSE="richardson"
+KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}"/${MY_P}.src
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-as-needed.patch
+	tc-export CC
+}
+
+src_install() {
+	dobin "${S}"/probe
+	dodoc "${S}"/README*
+}