commit: 1d628ae01ed5cc7b4bf4502efab58fc104589428 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Mon Aug 30 17:16:11 2021 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Mon Aug 30 17:38:49 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1d628ae0
sci-biology/njplot: Remove last-rited package Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/njplot/Manifest | 1 - .../njplot/files/njplot-2.3-buildsystem.patch | 59 ---------------------- .../njplot/files/njplot-2.3-format-security.patch | 16 ------ sci-biology/njplot/metadata.xml | 15 ------ sci-biology/njplot/njplot-2.3-r2.ebuild | 38 -------------- 6 files changed, 130 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 484e5b1182a..a91a2a5b53e 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -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 Revdeps are unmaintained too and out of date.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 <dilfri...@gentoo.org> (2021-07-31) # Obsolete; all versions in current Perl core distributions 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-biol...@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 -}
