From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- 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 | 12 +++++ sci-biology/njplot/njplot-2.3-r1.ebuild | 35 +++++++++++++ sci-biology/njplot/njplot-2.3.ebuild | 34 +++++++++++++ 6 files changed, 157 insertions(+) create mode 100644 sci-biology/njplot/Manifest create mode 100644 sci-biology/njplot/files/njplot-2.3-buildsystem.patch create mode 100644 sci-biology/njplot/files/njplot-2.3-format-security.patch create mode 100644 sci-biology/njplot/metadata.xml create mode 100644 sci-biology/njplot/njplot-2.3-r1.ebuild create mode 100644 sci-biology/njplot/njplot-2.3.ebuild (limited to 'sci-biology/njplot') diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest new file mode 100644 index 000000000000..17c26994a8c4 --- /dev/null +++ b/sci-biology/njplot/Manifest @@ -0,0 +1 @@ +DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca 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/metadata.xml b/sci-biology/njplot/metadata.xml new file mode 100644 index 000000000000..31592430880f --- /dev/null +++ b/sci-biology/njplot/metadata.xml @@ -0,0 +1,12 @@ + + + + sci-biology + + 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. + + 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..f766af55ea96 --- /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 +# $Id$ + +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 new file mode 100644 index 000000000000..03bcad009906 --- /dev/null +++ b/sci-biology/njplot/njplot-2.3.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +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-${PV}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="amd64 x86" +IUSE="" + +RDEPEND=" + sci-biology/ncbi-tools[X,static-libs] + x11-libs/libXmu" +DEPEND="${RDEPEND}" + +src_prepare() { + sed -i -e 's|/banques0/ncbiJun04|/usr/include/ncbi|' \ + -e 's/CC = gcc/CC='$(tc-getCC)'/' -e 's/CFLAGS =/CFLAGS +=/' \ + makefile || die + sed -i -e "s%njplot.help%/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die +} + +src_install() { + dobin newicktops newicktotxt njplot unrooted || die + doman *.1 || die + dodoc README njplot.help +} -- cgit v1.2.3-65-gdbad