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

6 files changed, 157 insertions, 0 deletions

diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest
new file mode 100644
index 000000000000..17c26994a8c4
--- /dev/null
+++ b/sci-biology/njplot/Manifest
@@ -0,0 +1 @@
+DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca
diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
new file mode 100644
index 000000000000..61f8b95ea160
--- /dev/null
+++ b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
@@ -0,0 +1,59 @@
+ makefile | 16 ++++++++--------
+ 1 file changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/makefile b/makefile
+index ccb7dc2..9488c2a 100644
+--- a/makefile
++++ b/makefile
+@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF
+ #PDFLIB = -L$(PDF) -lpdf
+ 
+ # c compiler and linker
+-CC = gcc
++CC ?= gcc
+ 
+ # Vibrant top directory
+-VIBRANT = /banques0/ncbiJun04
++VIBRANT = /usr/include/ncbi
+ 
+ 
+ # X11 include directory
+@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o
+ OBJUNROOTED = unrooted-vib.o preptree.o
+ 
+ 
+-CFLAGS  = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
++CFLAGS  += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \
+ 	-I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \
+-	-Wimplicit-function-declaration -g
++	-Wimplicit-function-declaration
+ 	
+ all: njplot  unrooted newicktops newicktotxt
+ 
+ 
+ njplot : $(OBJECTS)
+-	$(CC) -g -o njplot $(OBJECTS) \
++	$(CC) $(LDFLAGS) -o njplot $(OBJECTS) \
+         -L$(VIBRANT)/lib \
+         -lvibrant -lncbi \
+         $(PDFLIB)   \
+@@ -40,16 +40,16 @@ njplot : $(OBJECTS)
+         -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm
+         
+ unrooted : $(OBJUNROOTED)
+-	$(CC) -g -o unrooted $(OBJUNROOTED) \
++	$(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \
+         -L$(VIBRANT)/lib -lvibrant -lncbi \
+         -L$(MOTIFLIB) -lXm \
+         -L/usr/X11R6/lib -lXmu -lXt -lX11  -lm
+ 
+ newicktops: njplot-vib.c
+-	$(CC) -DNO_GUI  -DNO_PDF -o $@ njplot-vib.c -lm
++	$(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI  -DNO_PDF -o $@ njplot-vib.c -lm
+ 
+ newicktotxt: njplot-vib.c
+-	$(CC) -DTTY  -o $@ njplot-vib.c -lm
++	$(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm
+ 
+ 
+ .c.o : 
diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch
new file mode 100644
index 000000000000..686b8475e9ed
--- /dev/null
+++ b/sci-biology/njplot/files/njplot-2.3-format-security.patch
@@ -0,0 +1,16 @@
+ njplot-vib.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/njplot-vib.c b/njplot-vib.c
+index fe55609..63fd3b6 100644
+--- a/njplot-vib.c
++++ b/njplot-vib.c
+@@ -1976,7 +1976,7 @@ PDFONLY"       no window interface, just write the PDF/PostScript tree plot\n"
+ #else
+ 		fprintf(stderr,
+ #endif
+-		message);
++		"%s", message);
+ 		exit(0);
+ 		}
+ 	}
diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml
new file mode 100644
index 000000000000..31592430880f
--- /dev/null
+++ b/sci-biology/njplot/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <longdescription>
+		NJplot is a tree drawing program able to draw any phylogenetic tree
+		expressed in the Newick phylogenetic tree format (e.g., the format used
+		by the PHYLIP package). NJplot is especially convenient for rooting the
+		unrooted trees obtained from parsimony, distance or maximum likelihood
+		tree-building methods.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/njplot/njplot-2.3-r1.ebuild b/sci-biology/njplot/njplot-2.3-r1.ebuild
new file mode 100644
index 000000000000..f766af55ea96
--- /dev/null
+++ b/sci-biology/njplot/njplot-2.3-r1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+	sci-biology/ncbi-tools[X,static-libs]
+	x11-libs/libXmu"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	sed -i -e "s%njplot.help%${EPREFIX}/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die
+	epatch \
+		"${FILESDIR}"/${P}-format-security.patch \
+		"${FILESDIR}"/${P}-buildsystem.patch
+	tc-export CC
+}
+
+src_install() {
+	dobin newicktops newicktotxt njplot unrooted
+	doman *.1
+	dodoc README njplot.help
+}
diff --git a/sci-biology/njplot/njplot-2.3.ebuild b/sci-biology/njplot/njplot-2.3.ebuild
new file mode 100644
index 000000000000..03bcad009906
--- /dev/null
+++ b/sci-biology/njplot/njplot-2.3.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit toolchain-funcs
+
+DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting"
+HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html"
+SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+RDEPEND="
+	sci-biology/ncbi-tools[X,static-libs]
+	x11-libs/libXmu"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	sed -i -e 's|/banques0/ncbiJun04|/usr/include/ncbi|' \
+		-e 's/CC = gcc/CC='$(tc-getCC)'/' -e 's/CFLAGS  =/CFLAGS +=/' \
+		makefile || die
+	sed -i -e "s%njplot.help%/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die
+}
+
+src_install() {
+	dobin newicktops newicktotxt njplot unrooted || die
+	doman *.1 || die
+	dodoc README njplot.help
+}