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

8 files changed, 416 insertions, 0 deletions

diff --git a/sci-chemistry/raster3d/Manifest b/sci-chemistry/raster3d/Manifest
new file mode 100644
index 00000000000..fbf2feb05ff
--- /dev/null
+++ b/sci-chemistry/raster3d/Manifest
@@ -0,0 +1,2 @@
+DIST Raster3D_3.0-2.tar 1743034 SHA256 a89bdfda61fae8d189820941f1b5685b40743b817128f57bc1225f983a47d984 SHA512 f8f73cc91eae521839a9db8ee1a7a9d8727ed510cb574116d89e918480700d844691a6fc3c4a28cb54312b0133cc610422e55d99716803cf3e8bb5d9d934e37f WHIRLPOOL 58fc31cc438538715b1f0ea17a28b44294d78db32e40fa16f8ab5a5781e26198227c534f06b8d25072e6c6101a4c9255fa906b9fee57b128d0e767bc0e04db83
+DIST Raster3D_3.0-3.tar 1729356 SHA256 1e7d02cf17f2d14855b8d241269948b37ed4d3ae6395914b66ff9f95c3a7fecf SHA512 bd372c4ba8d40db38e19f520883ca71ab7c5ef7a451b67150894e229b45167dfe00b77c19e118afc6abdb9ac07800cc16de5d2dc82c3ef9baa751200490e40fa WHIRLPOOL ad7c11cfd42543845420dcffbc87024c60b3058a51663076ace63b2e2fc0fec81a342f7b4e54f535e03de14fb9e76eace65259cdd2e83a6e0e83810ac8280c10
diff --git a/sci-chemistry/raster3d/files/2.9.1-as-needed.patch b/sci-chemistry/raster3d/files/2.9.1-as-needed.patch
new file mode 100644
index 00000000000..2139804c896
--- /dev/null
+++ b/sci-chemistry/raster3d/files/2.9.1-as-needed.patch
@@ -0,0 +1,41 @@
+diff --git a/Makefile b/Makefile
+index e75ffcf..bcdd05c 100644
+--- a/Makefile
++++ b/Makefile
+@@ -188,7 +188,7 @@ avs2ps:	avs2ps.c
+ 	$(CC) $(CFLAGS) $(FLAGS) $(LDFLAGS) -o avs2ps avs2ps.c -lm
+ 
+ balls:	balls.f
+-	$(FC) $(FFLAGS) -o balls balls.f 
++	$(FC) $(LDFLAGS) $(FFLAGS) -o balls balls.f
+ 
+ local.o:	Makefile.incl local.c
+ 	$(CC) $(CFLAGS) $(FLAGS) -c local.c
+@@ -201,21 +201,18 @@ ribbon:	ribbon.f ribbon1.f modsubs.f
+ 	ribbon.f ribbon1.f modsubs.f -o ribbon
+ 
+ rastep:	rastep.f quadric.o suv.o
+-	$(FC) $(FFLAGS) \
+-	rastep.f quadric.o suv.o $(LDFLAGS) \
+-	-o rastep 
++	$(FC) $(FFLAGS) $(LDFLAGS) -o rastep \
++	rastep.f quadric.o suv.o
+ 
+ render:	render.o local.o quadric.o parse.o r3dtops.o ungz.o qinp.o
+-	$(FC) $(FFLAGS) \
++	$(FC) $(FFLAGS) $(LDFLAGS) -o render \
+ 	render.o local.o quadric.o parse.o r3dtops.o ungz.o \
+ 	qinp.o \
+-	$(LIBS) $(LDFLAGS) \
+-	-o render
++	$(LIBS)
+ 
+ normal3d:	normal3d.o quadric.o qinp.o ungz.o parameters.incl
+-	$(FC) $(FFLAGS) \
+-	normal3d.o quadric.o ungz.o qinp.o $(LDFLAGS) \
+-	-o normal3d
++	$(FC) $(FFLAGS) $(LDFLAGS) -o normal3d \
++	normal3d.o quadric.o ungz.o qinp.o
+ 
+ stereo3d:
+ 
diff --git a/sci-chemistry/raster3d/files/3.0.2-as-needed.patch b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch
new file mode 100644
index 00000000000..9e096195253
--- /dev/null
+++ b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch
@@ -0,0 +1,50 @@
+diff --git a/Makefile b/Makefile
+index 1a1c549..4d74dd0 100644
+--- a/Makefile
++++ b/Makefile
+@@ -58,7 +58,7 @@ linux:
+ 	@echo OSDEFS =  -DLINUX -DNETWORKBYTEORDER       >> Makefile.incl
+ 	@echo include Makefile.package        >> Makefile.incl
+ 	@echo                                 >> Makefile.incl
+-	@echo qinp.o: qinp.f                  >> Makefile.incl
++	@echo qinp.o: qinp.f normal3d.o render.o >> Makefile.incl
+ 	@echo "	\$$(FC) -g -O0 -Wall -Wtabs -c -o qinp.o qinp.f" >> Makefile.incl
+ 	@echo                                 >> Makefile.incl
+ 
+@@ -214,20 +214,20 @@ ribbon:	ribbon.f ribbon1.f modsubs.f
+ 	ribbon.f ribbon1.f modsubs.f -o ribbon
+ 
+ rastep:	rastep.f quadric.o suv.o
+-	$(FC) $(FFLAGS) \
+-	rastep.f quadric.o suv.o $(LDFLAGS) \
++	$(FC) $(FFLAGS) $(LDFLAGS) \
++	rastep.f quadric.o suv.o \
+ 	-o rastep 
+ 
+ render:	render.o local.o quadric.o parse.o r3dtogd.o ungz.o qinp.o
+-	$(FC) $(FFLAGS) \
++	$(FC) $(FFLAGS) $(LDFLAGS) \
+ 	render.o local.o quadric.o parse.o r3dtogd.o ungz.o \
+ 	qinp.o \
+-	$(LIBS) $(LDFLAGS) \
+-	-o render
++	-o render \
++	$(LIBS)
+ 
+ normal3d:	normal3d.o quadric.o qinp.o ungz.o parameters.incl
+-	$(FC) $(FFLAGS) \
+-	normal3d.o quadric.o ungz.o qinp.o $(LDFLAGS) \
++	$(FC) $(FFLAGS) $(LDFLAGS) \
++	normal3d.o quadric.o ungz.o qinp.o \
+ 	-o normal3d
+ 
+ stereo3d:
+@@ -264,7 +264,7 @@ example1.png: render_small
+ 	./render_small
+ 
+ render_small: render_small.o local.o quadric.o parse_small.o r3dtogd.o ungz.o qinp_small.o
+-	$(FC) $(FFLAGS) $^ $(LIBS) $(LDFLAGS) -o $@
++	$(FC) $(FFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
+ 
+ .SUFFIXES: .incl
+ SMALL=10
diff --git a/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch
new file mode 100644
index 00000000000..19b6cac3a6f
--- /dev/null
+++ b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch
@@ -0,0 +1,24 @@
+diff --git a/Makefile.template b/Makefile.template
+index 59de553..0ed283d 100644
+--- a/Makefile.template
++++ b/Makefile.template
+@@ -8,15 +8,15 @@ include VERSION
+ #
+ # Where to install the program, data files, and manuals
+ #
+-prefix  = /usr/local
++prefix  = @GENTOO_PORTAGE_EPREFIX@/usr/
+ bindir  = $(prefix)/bin
+ datadir = $(prefix)/share/Raster3D/materials
+ mandir  = $(prefix)/man/manl
+-htmldir = $(prefix)/share/Raster3D/html
++htmldir = $(prefix)/share/doc/MYPF/html
+ examdir = $(prefix)/share/Raster3D/examples
+ 
+-INCDIRS  =	-I/usr/include -I/usr/local/include
+-LIBDIRS  =	-L/usr/local/lib
++INCDIRS  =	-I@GENTOO_PORTAGE_EPREFIX@/usr/include
++LIBDIRS  =	-L@GENTOO_PORTAGE_EPREFIX@/usr/MYLIB
+ 
+ #
+ # TIFF support (enabled by default)
diff --git a/sci-chemistry/raster3d/files/raster3d-gcc-4.1-gentoo.patch b/sci-chemistry/raster3d/files/raster3d-gcc-4.1-gentoo.patch
new file mode 100644
index 00000000000..4525f5fdc8b
--- /dev/null
+++ b/sci-chemistry/raster3d/files/raster3d-gcc-4.1-gentoo.patch
@@ -0,0 +1,74 @@
+diff -Naur Raster3D_2.7c/normal3d.f Raster3D_2.7c.new/normal3d.f
+--- Raster3D_2.7c/normal3d.f	2003-10-20 18:50:11.000000000 -0400
++++ Raster3D_2.7c.new/normal3d.f	2007-09-08 10:23:08.000000000 -0400
+@@ -443,7 +443,8 @@
+ 	READ (INPUT,'(A)',ERR=101) TITLE
+ 	IF (TITLE(1:1).EQ.'#') GOTO 100
+ 	GOTO 102
+-  101	WRITE (NOISE,'(A,A)') ' >> Cannot open or read file ',TITLE(2:132)
++  101	WRITE (NOISE,'(A,A)') ' >> Cannot open or read file ',
++     * TITLE(2:132)
+ 	CALL EXIT(-1)
+   102	CONTINUE
+       ENDIF
+diff -Naur Raster3D_2.7c/parse.f Raster3D_2.7c.new/parse.f
+--- Raster3D_2.7c/parse.f	2003-10-20 18:50:11.000000000 -0400
++++ Raster3D_2.7c.new/parse.f	2007-09-08 10:23:48.000000000 -0400
+@@ -4,7 +4,8 @@
+       COMMON /OPTIONS/ FONTSCALE, GAMMA, ZOOM, NSCHEME, SHADOWFLAG, XBG, 
+      &                 NAX, NAY, OTMODE, QUALITY, INVERT, LFLAG
+       REAL             FONTSCALE, GAMMA, ZOOM
+-      INTEGER          NSCHEME, SHADOWFLAG, XBG
++      INTEGER          NSCHEME, SHADOWFLAG 
++      INTEGER*8        XBG
+       INTEGER*2        NAX, NAY, OTMODE, QUALITY
+       LOGICAL*2        INVERT, LFLAG
+ c
+diff -Naur Raster3D_2.7c/rastep.f Raster3D_2.7c.new/rastep.f
+--- Raster3D_2.7c/rastep.f	2004-02-12 12:01:31.000000000 -0500
++++ Raster3D_2.7c.new/rastep.f	2007-09-08 10:23:08.000000000 -0400
+@@ -133,7 +133,7 @@
+ c
+ c     Support for validation of similarity of bonded atoms
+       logical	suvflag
+-      integer	suvlun, suvbad
++      integer	suvlun, suvbad, defcols
+       real	anisov(6)
+ c
+ c     Default to CPK colors and VDW radii
+diff -Naur Raster3D_2.7c/render.f Raster3D_2.7c.new/render.f
+--- Raster3D_2.7c/render.f	2003-10-20 18:50:11.000000000 -0400
++++ Raster3D_2.7c.new/render.f	2007-09-08 10:23:08.000000000 -0400
+@@ -792,9 +792,9 @@
+ *     Get background colour
+       READ (INPUT,*,ERR=104) BKGND
+       if (XBG.NE.0) then
+-	BKGND(3) = FLOAT(iand(XBG,'00FF'X)) / 255.
+-	BKGND(2) = FLOAT(iand(XBG,'FF00'X)/256) / 255.
+-	BKGND(1) = FLOAT(iand(XBG,'FF0000'X)/65536) / 255.
++	BKGND(3) = REAL(iand(XBG,'00FF'X)) / 255.
++	BKGND(2) = REAL(iand(XBG,'FF00'X)/256) / 255.
++	BKGND(1) = REAL(iand(XBG,'FF0000'X)/65536) / 255.
+ 	BKGND(3) = BKGND(3)**2
+ 	BKGND(2) = BKGND(2)**2
+ 	BKGND(1) = BKGND(1)**2
+@@ -3679,7 +3679,7 @@
+ 	        FRAC = DETAIL(K+8)
+ 	        INEXT = INDTOP + 1
+   	        IF (TYPE(INEXT).EQ.VERTEXRGB) INEXT = INEXT + 1
+-	        CALL ASSERT(TYPE(INEXT).EQ.VERTRANSP,'lost vertex transp')
++	    CALL ASSERT(TYPE(INEXT).EQ.VERTRANSP,'lost vertex transp')
+ 	        K = LIST(INEXT)
+ 	        CLRITY = FRAC*DETAIL(K+1) + (1.-FRAC)*DETAIL(K+2)
+ 	      ELSE IF (TYPE(INDTOP).EQ.TRIANG) THEN
+diff -Naur Raster3D_2.7c/rings3d.f Raster3D_2.7c.new/rings3d.f
+--- Raster3D_2.7c/rings3d.f	2003-10-20 18:50:11.000000000 -0400
++++ Raster3D_2.7c.new/rings3d.f	2007-09-08 10:23:08.000000000 -0400
+@@ -16,7 +16,6 @@
+ 	integer input, output, noise
+ 	parameter (input=5, output=6, noise=0)
+ 	integer 	iargc, narg
+-	external	iargc
+ 	character*64	options
+ 	logical		bflag, pflag, sflag
+ c
diff --git a/sci-chemistry/raster3d/metadata.xml b/sci-chemistry/raster3d/metadata.xml
new file mode 100644
index 00000000000..2a6e4b56f96
--- /dev/null
+++ b/sci-chemistry/raster3d/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-chemistry</herd>
+  <upstream>
+    <changelog>http://skuld.bmsc.washington.edu/raster3d/CHANGELOG</changelog>
+  </upstream>
+  <use>
+    <flag name="gd">libgd support for PNG and JPEG output</flag>
+  </use>
+</pkgmetadata>
diff --git a/sci-chemistry/raster3d/raster3d-3.0.2.ebuild b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild
new file mode 100644
index 00000000000..380f207260e
--- /dev/null
+++ b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild
@@ -0,0 +1,107 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix
+
+MY_PN="Raster3D"
+MY_PV=$(replace_version_separator 2 -)
+MY_P="${MY_PN}_${MY_PV}"
+
+DESCRIPTION="Generation high quality raster images of proteins or other molecules"
+HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html"
+SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar"
+
+LICENSE="Artistic-2"
+SLOT="0"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+IUSE="gd tiff"
+
+RDEPEND="
+	tiff? ( media-libs/tiff:0 )
+	gd? ( media-libs/gd[jpeg,png] )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-as-needed.patch \
+		"${FILESDIR}"/${PV}-gentoo-prefix.patch
+
+	sed \
+		-e "s:MYPF:${PF}:" \
+		-e "s:MYLIB:$(get_libdir):g" \
+		-i Makefile.template || \
+		die "Failed to patch makefile.template"
+
+	if ! use gd; then
+		sed \
+			-e "/GDLIBS/s:^:#:g" \
+			-e "/GDDEFS/s:^:#:g" \
+			-i Makefile.template || die
+	fi
+
+	if ! use tiff; then
+		sed \
+			-e "/TLIBS/s:^:#:g" \
+			-e "/TDEFS/s:^:#:g" \
+			-i Makefile.template || die
+	fi
+
+	if [[ $(tc-getFC) =~ gfortran ]]; then
+		append-cflags -Dgfortran
+	fi
+
+	append-fflags -ffixed-line-length-132
+
+	eprefixify Makefile.template
+	cp Makefile.template Makefile.incl || die
+}
+
+src_compile() {
+	local target
+	local i
+
+	if [[ $(tc-getFC) =~ gfortran ]]; then
+		target="linux"
+	else
+		target="linux-$(tc-getFC)"
+	fi
+
+	for i in render.o ${target} all; do
+		emake \
+			CFLAGS="${CFLAGS}" \
+			LDFLAGS="${LDFLAGS}" \
+			FFLAGS="${FFLAGS}" \
+			CC="$(tc-getCC)"\
+			FC="$(tc-getFC)" \
+			INCDIRS="-I${EPREFIX}/usr/include" \
+			LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \
+			${i}
+	done
+}
+
+src_install() {
+	emake prefix="${ED}"/usr \
+			bindir="${ED}"/usr/bin \
+			datadir="${ED}"/usr/share/Raster3D/materials \
+			mandir="${ED}"/usr/share/man/man1 \
+			htmldir="${ED}"/usr/share/doc/${PF}/html \
+			examdir="${ED}"/usr/share/Raster3D/examples \
+			install
+
+	dodir /etc/env.d
+	echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \
+		"${ED}"/etc/env.d/10raster3d || \
+		die "Failed to install env file."
+}
+
+pkg_postinst() {
+	elog "Add following line:"
+	elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />"
+	elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml"
+	elog "to make imagemagick use raster3d for .r3d files"
+}
diff --git a/sci-chemistry/raster3d/raster3d-3.0.3.ebuild b/sci-chemistry/raster3d/raster3d-3.0.3.ebuild
new file mode 100644
index 00000000000..d66a807cbbf
--- /dev/null
+++ b/sci-chemistry/raster3d/raster3d-3.0.3.ebuild
@@ -0,0 +1,107 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix
+
+MY_PN="Raster3D"
+MY_PV=$(replace_version_separator 2 -)
+MY_P="${MY_PN}_${MY_PV}"
+
+DESCRIPTION="Generation high quality raster images of proteins or other molecules"
+HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html"
+SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar"
+
+LICENSE="Artistic-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="gd tiff"
+
+RDEPEND="
+	tiff? ( media-libs/tiff:0 )
+	gd? ( media-libs/gd[jpeg,png] )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/3.0.2-as-needed.patch \
+		"${FILESDIR}"/3.0.2-gentoo-prefix.patch
+
+	sed \
+		-e "s:MYPF:${PF}:" \
+		-e "s:MYLIB:$(get_libdir):g" \
+		-i Makefile.template || \
+		die "Failed to patch makefile.template"
+
+	if ! use gd; then
+		sed \
+			-e "/GDLIBS/s:^:#:g" \
+			-e "/GDDEFS/s:^:#:g" \
+			-i Makefile.template || die
+	fi
+
+	if ! use tiff; then
+		sed \
+			-e "/TLIBS/s:^:#:g" \
+			-e "/TDEFS/s:^:#:g" \
+			-i Makefile.template || die
+	fi
+
+	if [[ $(tc-getFC) =~ gfortran ]]; then
+		append-cflags -Dgfortran
+	fi
+
+	append-fflags -ffixed-line-length-132
+
+	eprefixify Makefile.template
+	cp Makefile.template Makefile.incl || die
+}
+
+src_compile() {
+	local target
+	local i
+
+	if [[ $(tc-getFC) =~ gfortran ]]; then
+		target="linux"
+	else
+		target="linux-$(tc-getFC)"
+	fi
+
+	for i in render.o ${target} all; do
+		emake \
+			CFLAGS="${CFLAGS}" \
+			LDFLAGS="${LDFLAGS}" \
+			FFLAGS="${FFLAGS}" \
+			CC="$(tc-getCC)"\
+			FC="$(tc-getFC)" \
+			INCDIRS="-I${EPREFIX}/usr/include" \
+			LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \
+			${i}
+	done
+}
+
+src_install() {
+	emake prefix="${ED}"/usr \
+			bindir="${ED}"/usr/bin \
+			datadir="${ED}"/usr/share/Raster3D/materials \
+			mandir="${ED}"/usr/share/man/man1 \
+			htmldir="${ED}"/usr/share/doc/${PF}/html \
+			examdir="${ED}"/usr/share/Raster3D/examples \
+			install
+
+	dodir /etc/env.d
+	echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \
+		"${ED}"/etc/env.d/10raster3d || \
+		die "Failed to install env file."
+}
+
+pkg_postinst() {
+	elog "Add following line:"
+	elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />"
+	elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml"
+	elog "to make imagemagick use raster3d for .r3d files"
+}