gentoo resync : 31.08.2021

5 files changed, 0 insertions, 133 deletions

diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest
deleted file mode 100644
index 22b172beb6c7..000000000000
--- a/sci-biology/njplot/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX njplot-2.3-buildsystem.patch 1688 BLAKE2B 06d03338d02efc2b13985148f784472afbe27855fc3a0da9e8194dcf16337a320ccacc2de43a9daf6eb2eb4df172fbde4ea4777caa4f5edf58ddc9234a022386 SHA512 af7f9c4e7e20f80e66e78eefb93dce0f99594987fc9ce04de0f447c03e2523b152bd5d32459ab075ca7a65da5d2fb4bb7624e7048f1d6a9ac7c3e1d4b28927b3
-AUX njplot-2.3-format-security.patch 366 BLAKE2B 63160d8d6774d8dd802118cb8e40849545dc6b7522afd539cbe8861bc52309e70e06969a5a35786671c2ee3da77850923e0d4651582050699ec5c7159cbf16eb SHA512 1a6a3d823eebca79da482c534f4c7e54e025900dd6f8407a9ae50e997c3585301762da1b0bdd2311f6b5698ba33d96a8fca6b8fada541323a97773146ef8e773
-DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059
-EBUILD njplot-2.3-r2.ebuild 847 BLAKE2B c681b44afb880e275afef70df7b6d14a36853c49872be1296c639e7c0ae1a358f3ebdd76294dce86392d5c75f01bee19c075c2533ff3b21c12f5e4769f032c26 SHA512 8a67dfe8db133776ea7bec00d376c0b25e4044916b1d67659b1a3a8a80c68ef7a90d91005e009acb48fa3f486c7611352639f00067d514cca93a32227a243eb4
-MISC metadata.xml 616 BLAKE2B 6b63329645cb512061e44565357fa2339303f98ebd34b6c7d39159dd61cb1997401500ec5c7db82e7c8a0792e0fbc46bd92fb350c5cc711f076e4dceb5ddd1a5 SHA512 828535cff695925a319a6180a904ec8ad35c387e684e4fafd8d86e9978fcba8dc151e8a3e191b6f8b6b75d29ed3352cc34e2adf325dc5a663b170724df48b771
diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
deleted file mode 100644
index 61f8b95ea160..000000000000
--- a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch
+++ /dev/null
@@ -1,59 +0,0 @@
- 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
deleted file mode 100644
index 686b8475e9ed..000000000000
--- a/sci-biology/njplot/files/njplot-2.3-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- 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
deleted file mode 100644
index 2a3eb3140966..000000000000
--- a/sci-biology/njplot/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<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-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild
deleted file mode 100644
index 420861dac42b..000000000000
--- a/sci-biology/njplot/njplot-2.3-r2.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-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"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	sci-biology/ncbi-tools[X,static-libs]
-	x11-libs/libXmu"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-format-security.patch
-	"${FILESDIR}"/${P}-buildsystem.patch
-)
-
-src_prepare() {
-	default
-	sed -i -e "s:njplot.help:${EPREFIX}/usr/share/doc/${PF}/njplot.help:" njplot-vib.c || die
-
-	tc-export CC
-}
-
-src_install() {
-	dobin newicktops newicktotxt njplot unrooted
-	doman *.1
-	dodoc README njplot.help
-}