From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/njplot/Manifest | 7 +++ .../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 ++++++++++++++ 5 files changed, 135 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-r2.ebuild (limited to 'sci-biology/njplot') diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest new file mode 100644 index 000000000000..b90b24102bec --- /dev/null +++ b/sci-biology/njplot/Manifest @@ -0,0 +1,7 @@ +AUX njplot-2.3-buildsystem.patch 1688 SHA256 2ebdf312755f1bb6915ff93959329fa20f92e2b00d681b104858d98e397f2cfb SHA512 af7f9c4e7e20f80e66e78eefb93dce0f99594987fc9ce04de0f447c03e2523b152bd5d32459ab075ca7a65da5d2fb4bb7624e7048f1d6a9ac7c3e1d4b28927b3 WHIRLPOOL 740210f26125ba444544a4394841e16e8e5c584b19ae047faedf7afcc24033caf44b615c7b21c77623efe380a6d34c42a9c46f46b25082a18acb425748478450 +AUX njplot-2.3-format-security.patch 366 SHA256 99bbf3411f8584b3cfbfbeac2c81c3b46ebda7de96279d7a1a0fc625bdec5732 SHA512 1a6a3d823eebca79da482c534f4c7e54e025900dd6f8407a9ae50e997c3585301762da1b0bdd2311f6b5698ba33d96a8fca6b8fada541323a97773146ef8e773 WHIRLPOOL a9736eb7047530d28073791924d79ef9ed65df051cc65b7e432fa9a8abd703131e2f5343266738b7727d43ffca1a918fd2341256aca5472e21a8e0a0e28be856 +DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca +EBUILD njplot-2.3-r2.ebuild 847 SHA256 737901f1562015722d18b658ca43e5de166098a0c393516e38159433c5e9e41e SHA512 8a67dfe8db133776ea7bec00d376c0b25e4044916b1d67659b1a3a8a80c68ef7a90d91005e009acb48fa3f486c7611352639f00067d514cca93a32227a243eb4 WHIRLPOOL 5880a2828b98c1585907354a3fcd50f8298cca8bd557d5ff513cd3398271567c4b20227bad12fbf74498440ae30adaf8fd06bf630cb34fdf74618f73881c433d +MISC ChangeLog 2557 SHA256 e9561fdc8d0a5aec7df0672ed1faca36e91d11656ab7a7de8cfbc09600b42679 SHA512 e0ec62d00ab79b62802ca874215a4f78889b7f5706e135b7a27b04b034547fd001f88efbe3b986604de60848c500afa9723ebf6560b0755ee4ef48b350fe7bcc WHIRLPOOL 8f2297579749ee5079b0d6d7ddefc4af9ebdd871a564ec348fd536acd7cd11ff1cb6e0fbdd84dccde0da93e000ab61c9cc01dfd91ef9cfb7efff3d2600f2eb20 +MISC ChangeLog-2015 2256 SHA256 4958d1e7fa4caf5f2ad1ba69e7f8daf40ed151d58c0a6808956f09cb8a23c0bb SHA512 06c63bb851ce2f5bd3e6fd5aa58d0a46da8940eb81e99fd061cc9f8e3ee8093933d67b8f8c89264a54fa83d3531dcf2e18265b3894c09414f3eac8bb45884d23 WHIRLPOOL 2fd74b27c91b66c91cfa9455365a259e797470b747800d523c87de9192ab0c93794c5742e595d9258ca97f0d0f946f78ed0c67da63e641c54d2ddb3ae873500e +MISC metadata.xml 623 SHA256 a62d170844dfa49cc9e1b16e6316f6681be21207953d7b4a3332e35b6c69a4fe SHA512 494c11097c9484cfb104a8da218202294d13e71b2a8216342c7b9b7f00a97ac19403a3f21db91de08bc38e1bbed39693bd13167b70daad40267dca5fa30e2ff1 WHIRLPOOL 7e0336a4e039f1d4d373ea044e4c46b7d893939f063c12626500d986bfe2d2e975e5e8214b8558cf87bfec1036bfcaf4cec318bbc8b2a5003b081917e94c6874 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 $@ njplot-vib.c -lm + + + .c.o : diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch new file mode 100644 index 000000000000..686b8475e9ed --- /dev/null +++ b/sci-biology/njplot/files/njplot-2.3-format-security.patch @@ -0,0 +1,16 @@ + njplot-vib.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/njplot-vib.c b/njplot-vib.c +index fe55609..63fd3b6 100644 +--- a/njplot-vib.c ++++ b/njplot-vib.c +@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" + #else + fprintf(stderr, + #endif +- message); ++ "%s", message); + exit(0); + } + } diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml new file mode 100644 index 000000000000..4cdb5abfd7a5 --- /dev/null +++ b/sci-biology/njplot/metadata.xml @@ -0,0 +1,15 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + NJplot is a tree drawing program able to draw any phylogenetic tree + expressed in the Newick phylogenetic tree format (e.g., the format used + by the PHYLIP package). NJplot is especially convenient for rooting the + unrooted trees obtained from parsimony, distance or maximum likelihood + tree-building methods. + + diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild new file mode 100644 index 000000000000..420861dac42b --- /dev/null +++ b/sci-biology/njplot/njplot-2.3-r2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${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 +} -- cgit v1.2.3