From 3b08f674e3f771b49370edb144dab0958c8cf721 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Tue, 31 Aug 2021 08:59:54 +0100 Subject: gentoo resync : 31.08.2021 --- sci-biology/njplot/Manifest | 5 -- .../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, 133 deletions(-) delete mode 100644 sci-biology/njplot/Manifest delete mode 100644 sci-biology/njplot/files/njplot-2.3-buildsystem.patch delete mode 100644 sci-biology/njplot/files/njplot-2.3-format-security.patch delete mode 100644 sci-biology/njplot/metadata.xml delete 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 deleted file mode 100644 index 22b172beb6c7..000000000000 --- a/sci-biology/njplot/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX njplot-2.3-buildsystem.patch 1688 BLAKE2B 06d03338d02efc2b13985148f784472afbe27855fc3a0da9e8194dcf16337a320ccacc2de43a9daf6eb2eb4df172fbde4ea4777caa4f5edf58ddc9234a022386 SHA512 af7f9c4e7e20f80e66e78eefb93dce0f99594987fc9ce04de0f447c03e2523b152bd5d32459ab075ca7a65da5d2fb4bb7624e7048f1d6a9ac7c3e1d4b28927b3 -AUX njplot-2.3-format-security.patch 366 BLAKE2B 63160d8d6774d8dd802118cb8e40849545dc6b7522afd539cbe8861bc52309e70e06969a5a35786671c2ee3da77850923e0d4651582050699ec5c7159cbf16eb SHA512 1a6a3d823eebca79da482c534f4c7e54e025900dd6f8407a9ae50e997c3585301762da1b0bdd2311f6b5698ba33d96a8fca6b8fada541323a97773146ef8e773 -DIST njplot-2.3.tar.gz 83641 BLAKE2B 3dd2798c190a103e88babb592cda184ae7ab4839cc779f739205480e2cce641bc9f8a57d20bd96ce8fc4a1e662a81de0bb13f2a4ffa9d03f8e0f286c762b993a SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 -EBUILD njplot-2.3-r2.ebuild 847 BLAKE2B c681b44afb880e275afef70df7b6d14a36853c49872be1296c639e7c0ae1a358f3ebdd76294dce86392d5c75f01bee19c075c2533ff3b21c12f5e4769f032c26 SHA512 8a67dfe8db133776ea7bec00d376c0b25e4044916b1d67659b1a3a8a80c68ef7a90d91005e009acb48fa3f486c7611352639f00067d514cca93a32227a243eb4 -MISC metadata.xml 616 BLAKE2B 6b63329645cb512061e44565357fa2339303f98ebd34b6c7d39159dd61cb1997401500ec5c7db82e7c8a0792e0fbc46bd92fb350c5cc711f076e4dceb5ddd1a5 SHA512 828535cff695925a319a6180a904ec8ad35c387e684e4fafd8d86e9978fcba8dc151e8a3e191b6f8b6b75d29ed3352cc34e2adf325dc5a663b170724df48b771 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 61f8b95ea160..000000000000 --- 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 $@ njplot-vib.c -lm - - - .c.o : diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch deleted file mode 100644 index 686b8475e9ed..000000000000 --- a/sci-biology/njplot/files/njplot-2.3-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - njplot-vib.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/njplot-vib.c b/njplot-vib.c -index fe55609..63fd3b6 100644 ---- a/njplot-vib.c -+++ b/njplot-vib.c -@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" - #else - fprintf(stderr, - #endif -- message); -+ "%s", message); - exit(0); - } - } diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml deleted file mode 100644 index 2a3eb3140966..000000000000 --- a/sci-biology/njplot/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - NJplot is a tree drawing program able to draw any phylogenetic tree - expressed in the Newick phylogenetic tree format (e.g., the format used - by the PHYLIP package). NJplot is especially convenient for rooting the - unrooted trees obtained from parsimony, distance or maximum likelihood - tree-building methods. - - diff --git a/sci-biology/njplot/njplot-2.3-r2.ebuild b/sci-biology/njplot/njplot-2.3-r2.ebuild deleted file mode 100644 index 420861dac42b..000000000000 --- a/sci-biology/njplot/njplot-2.3-r2.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" -HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" -SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${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 -} -- cgit v1.2.3