Fix dependencies, #425710; make buildsystem sane; fix format-security

Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

6 files changed, 148 insertions, 16 deletions

diff --git a/sci-biology/njplot/ChangeLog b/sci-biology/njplot/ChangeLog
index 0c34df81078f..dafa15c51099 100644
--- a/sci-biology/njplot/ChangeLog
+++ b/sci-biology/njplot/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/njplot
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/njplot/ChangeLog,v 1.12 2013/03/11 16:22:49 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/njplot/ChangeLog,v 1.13 2015/03/02 13:14:37 jlec Exp $
+
+*njplot-2.3-r1 (02 Mar 2015)
+
+  02 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +files/njplot-2.3-buildsystem.patch, +files/njplot-2.3-format-security.patch,
+  +njplot-2.3-r1.ebuild, njplot-2.3.ebuild:
+  Fix dependencies, #425710; make buildsystem sane; fix format-security
 
   11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -56,4 +63,3 @@
   06 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
   +njplot-unrooted-1.ebuild:
   Initial import.
-
diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest
index b9c08c0ae3f4..d00fbe593095 100644
--- a/sci-biology/njplot/Manifest
+++ b/sci-biology/njplot/Manifest
@@ -1,14 +1,29 @@
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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/njplot-2.3-r1.ebuild b/sci-biology/njplot/njplot-2.3-r1.ebuild
new file mode 100644
index 000000000000..3bee889df64d
--- /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
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/njplot/njplot-2.3-r1.ebuild,v 1.1 2015/03/02 13:14:37 jlec Exp $
+
+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
index 5c0fba327044..5cd48aadb673 100644
--- a/sci-biology/njplot/njplot-2.3.ebuild
+++ b/sci-biology/njplot/njplot-2.3.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/njplot/njplot-2.3.ebuild,v 1.2 2009/10/31 17:59:45 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/njplot/njplot-2.3.ebuild,v 1.3 2015/03/02 13:14:37 jlec Exp $
 
 EAPI="2"
 
@@ -9,15 +9,16 @@ 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"
-LICENSE="public-domain"
 
 SLOT="0"
+LICENSE="public-domain"
 KEYWORDS="amd64 x86"
 IUSE=""
 
-RDEPEND="x11-libs/libXmu"
-DEPEND="sci-biology/ncbi-tools[X]
-	${RDEPEND}"
+RDEPEND="
+	sci-biology/ncbi-tools[X,static-libs]
+	x11-libs/libXmu"
+DEPEND="${RDEPEND}"
 
 src_prepare() {
 	sed -i -e 's|/banques0/ncbiJun04|/usr/include/ncbi|' \