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sci-biology/njplot: Remove last-rited package

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Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
This commit is contained in:
Jakov Smolić
2021-08-30 19:16:11 +02:00
parent 5781aaa8b6
commit 1d628ae01e
6 changed files with 0 additions and 130 deletions
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1
profiles/package.mask
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@@ -285,7 +285,6 @@ sci-libs/sktime
# anymore, tons of bugs. Revdeps are unmaintained too and out of date.
# Bug #798015, removal in 30 days.
sci-biology/ncbi-tools
sci-biology/njplot
# Andreas K. Hüttel <dilfridge@gentoo.org> (2021-07-31)
# Obsolete; all versions in current Perl core distributions

1
sci-biology/njplot/Manifest
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@@ -1 +0,0 @@
DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059

59
sci-biology/njplot/files/njplot-2.3-buildsystem.patch
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@@ -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 :

16
sci-biology/njplot/files/njplot-2.3-format-security.patch
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@@ -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);
}
}

15
sci-biology/njplot/metadata.xml
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@@ -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>

38
sci-biology/njplot/njplot-2.3-r2.ebuild
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@@ -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
}