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authorJakov Smolić <jsmolic@gentoo.org>2021-08-30 19:16:11 +0200
committerJakov Smolić <jsmolic@gentoo.org>2021-08-30 19:38:49 +0200
commit1d628ae01ed5cc7b4bf4502efab58fc104589428 (patch)
tree679423bf2998d008aa44dff9406fa3407ee60cbb /sci-biology/njplot
parentsci-biology/psipred: Remove last-rited package (diff)
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sci-biology/njplot: Remove last-rited package
Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
Diffstat (limited to 'sci-biology/njplot')
-rw-r--r--sci-biology/njplot/Manifest1
-rw-r--r--sci-biology/njplot/files/njplot-2.3-buildsystem.patch59
-rw-r--r--sci-biology/njplot/files/njplot-2.3-format-security.patch16
-rw-r--r--sci-biology/njplot/metadata.xml15
-rw-r--r--sci-biology/njplot/njplot-2.3-r2.ebuild38
5 files changed, 0 insertions, 129 deletions
diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest
deleted file mode 100644
index 6cec177af40..00000000000
--- a/sci-biology/njplot/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059
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 61f8b95ea16..00000000000
--- 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 686b8475e9e..00000000000
--- 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 2a3eb314096..00000000000
--- 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 420861dac42..00000000000
--- 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
-}