From ee36ecf16f89cc2ea374cf69692b8630c32a6990 Mon Sep 17 00:00:00 2001 From: ben Date: Mon, 16 Aug 2004 23:58:35 +0000 Subject: Update phylip to version 3.61. No ChangeLog included. However there is a very long list of bux fixes since 3.57 at: http://evolution.genetics.washington.edu/phylip/bugs.html --- biology/phylip/DESCR | 5 +- biology/phylip/Makefile | 44 ++++++++++------- biology/phylip/PLIST | 106 ++++++++++++++++++++++------------------ biology/phylip/distinfo | 7 +-- biology/phylip/patches/patch-aa | 13 +++++ 5 files changed, 104 insertions(+), 71 deletions(-) create mode 100644 biology/phylip/patches/patch-aa (limited to 'biology') diff --git a/biology/phylip/DESCR b/biology/phylip/DESCR index 4207db17ffd..e23305e894a 100644 --- a/biology/phylip/DESCR +++ b/biology/phylip/DESCR @@ -1,3 +1,2 @@ - This is a FREE package of programs for inferring phylogenies and carrying -out certain related tasks. At present it contains 30 programs, which carry out -different algorithms on different kinds of data. +PHYLIP, the Phylogeny Inference Package, is a package of programs for +inferring phylogenies (evolutionary trees). diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile index 912ba1e7415..fe1e2b0e73a 100644 --- a/biology/phylip/Makefile +++ b/biology/phylip/Makefile @@ -1,11 +1,8 @@ -# $NetBSD: Makefile,v 1.6 2004/01/20 12:08:40 agc Exp $ +# $NetBSD: Makefile,v 1.7 2004/08/16 23:58:35 ben Exp $ -DISTNAME= phylip -PKGNAME= phylip-3.573c +DISTNAME= phylip-3.61 CATEGORIES= biology -MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ \ - ftp://ftp.bioss.sari.ac.uk/pub/phylogeny/phylip/ -EXTRACT_SUFX= .tar.Z +MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ MAINTAINER= babafou@babafou.eu.org HOMEPAGE= http://evolution.genetics.washington.edu/phylip.html @@ -15,25 +12,36 @@ RESTRICTED= "No commercial distribution without a royalty agreement with the au NO_SRC_ON_CDROM= ${RESTRICTED} NO_BIN_ON_CDROM= ${RESTRICTED} -WRKSRC= ${WRKDIR} +WRKSRC= ${WRKDIR}/${DISTNAME}/src + +MAKE_FLAGS+= CC=${CC} do-install: - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/phylip -.for DOC in main.doc \ - contchar.doc discrete.doc distance.doc draw.doc sequence.doc - ${INSTALL_DATA} ${WRKSRC}/${DOC} ${PREFIX}/share/doc/phylip -.endfor .for PROGRAM in clique consense contml contrast dnacomp dnadist \ dnainvar dnaml dnamlk dnamove dnapars dnapenny \ - dolmove dollop dolpenny drawgram drawtree factor \ - fitch gendist kitsch mix move neighbor penny \ - protdist protpars restml retree seqboot + dolmove dollop dolpenny factor fitch gendist kitsch \ + mix move neighbor pars penny proml promlk protdist \ + protpars restdist restml retree seqboot treedist \ + drawgram drawtree ${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin - ${INSTALL_DATA} ${WRKSRC}/${PROGRAM}.doc ${PREFIX}/share/doc/phylip .endfor - ${INSTALL_DATA_DIR} ${PREFIX}/share/misc/phylip + ${INSTALL_DATA_DIR} ${PREFIX}/share/fonts/phylip .for FONT in font1 font2 font3 font4 font5 font6 - ${INSTALL_DATA} ${WRKSRC}/${FONT} ${PREFIX}/share/misc/phylip + ${INSTALL_DATA} ${WRKSRC}/${FONT} ${PREFIX}/share/fonts/phylip +.endfor + ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/phylip +.for HTML in clique.html consense.html contchar.html contml.html \ + contrast.html discrete.html distance.html dnacomp.html \ + dnadist.html dnainvar.html dnaml.html dnamlk.html \ + dnamove.html dnapars.html dnapenny.html dollop.html \ + dolmove.html dolpenny.html draw.html drawgram.html \ + drawtree.html factor.html fitch.html gendist.html \ + kitsch.html main.html mix.html move.html neighbor.html \ + pars.html penny.html phylip.gif phylip.html proml.html \ + promlk.html protdist.html protpars.html restdist.html \ + restml.html retree.html seqboot.html sequence.html \ + treedist.html + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${HTML} ${PREFIX}/share/doc/html/phylip .endfor .include "../../mk/bsd.pkg.mk" diff --git a/biology/phylip/PLIST b/biology/phylip/PLIST index 17785800d18..3db2387aa70 100644 --- a/biology/phylip/PLIST +++ b/biology/phylip/PLIST @@ -1,75 +1,87 @@ -@comment $NetBSD: PLIST,v 1.1 2001/10/31 21:28:10 zuntum Exp $ -share/doc/phylip/main.doc -share/doc/phylip/contchar.doc -share/doc/phylip/discrete.doc -share/doc/phylip/distance.doc -share/doc/phylip/draw.doc -share/doc/phylip/sequence.doc +@comment $NetBSD: PLIST,v 1.2 2004/08/16 23:58:35 ben Exp $ bin/clique -share/doc/phylip/clique.doc bin/consense -share/doc/phylip/consense.doc bin/contml -share/doc/phylip/contml.doc bin/contrast -share/doc/phylip/contrast.doc bin/dnacomp -share/doc/phylip/dnacomp.doc bin/dnadist -share/doc/phylip/dnadist.doc bin/dnainvar -share/doc/phylip/dnainvar.doc bin/dnaml -share/doc/phylip/dnaml.doc bin/dnamlk -share/doc/phylip/dnamlk.doc bin/dnamove -share/doc/phylip/dnamove.doc bin/dnapars -share/doc/phylip/dnapars.doc bin/dnapenny -share/doc/phylip/dnapenny.doc bin/dolmove -share/doc/phylip/dolmove.doc bin/dollop -share/doc/phylip/dollop.doc bin/dolpenny -share/doc/phylip/dolpenny.doc -bin/drawgram -share/doc/phylip/drawgram.doc -bin/drawtree -share/doc/phylip/drawtree.doc bin/factor -share/doc/phylip/factor.doc bin/fitch -share/doc/phylip/fitch.doc bin/gendist -share/doc/phylip/gendist.doc bin/kitsch -share/doc/phylip/kitsch.doc bin/mix -share/doc/phylip/mix.doc bin/move -share/doc/phylip/move.doc bin/neighbor -share/doc/phylip/neighbor.doc +bin/pars bin/penny -share/doc/phylip/penny.doc +bin/proml +bin/promlk bin/protdist -share/doc/phylip/protdist.doc bin/protpars -share/doc/phylip/protpars.doc +bin/restdist bin/restml -share/doc/phylip/restml.doc bin/retree -share/doc/phylip/retree.doc bin/seqboot -share/doc/phylip/seqboot.doc -@dirrm share/doc/phylip -share/misc/phylip/font1 -share/misc/phylip/font2 -share/misc/phylip/font3 -share/misc/phylip/font4 -share/misc/phylip/font5 -share/misc/phylip/font6 -@dirrm share/misc/phylip +bin/treedist +bin/drawgram +bin/drawtree +share/doc/html/phylip/clique.html +share/doc/html/phylip/consense.html +share/doc/html/phylip/contchar.html +share/doc/html/phylip/contml.html +share/doc/html/phylip/contrast.html +share/doc/html/phylip/discrete.html +share/doc/html/phylip/distance.html +share/doc/html/phylip/dnacomp.html +share/doc/html/phylip/dnadist.html +share/doc/html/phylip/dnainvar.html +share/doc/html/phylip/dnaml.html +share/doc/html/phylip/dnamlk.html +share/doc/html/phylip/dnamove.html +share/doc/html/phylip/dnapars.html +share/doc/html/phylip/dnapenny.html +share/doc/html/phylip/dollop.html +share/doc/html/phylip/dolmove.html +share/doc/html/phylip/dolpenny.html +share/doc/html/phylip/draw.html +share/doc/html/phylip/drawgram.html +share/doc/html/phylip/drawtree.html +share/doc/html/phylip/factor.html +share/doc/html/phylip/fitch.html +share/doc/html/phylip/gendist.html +share/doc/html/phylip/kitsch.html +share/doc/html/phylip/main.html +share/doc/html/phylip/mix.html +share/doc/html/phylip/move.html +share/doc/html/phylip/neighbor.html +share/doc/html/phylip/pars.html +share/doc/html/phylip/penny.html +share/doc/html/phylip/phylip.gif +share/doc/html/phylip/phylip.html +share/doc/html/phylip/proml.html +share/doc/html/phylip/promlk.html +share/doc/html/phylip/protdist.html +share/doc/html/phylip/protpars.html +share/doc/html/phylip/restdist.html +share/doc/html/phylip/restml.html +share/doc/html/phylip/retree.html +share/doc/html/phylip/seqboot.html +share/doc/html/phylip/sequence.html +share/doc/html/phylip/treedist.html +@dirrm share/doc/html/phylip +share/fonts/phylip/font1 +share/fonts/phylip/font2 +share/fonts/phylip/font3 +share/fonts/phylip/font4 +share/fonts/phylip/font5 +share/fonts/phylip/font6 +@dirrm share/fonts/phylip diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo index 71745bce117..481872f389f 100644 --- a/biology/phylip/distinfo +++ b/biology/phylip/distinfo @@ -1,4 +1,5 @@ -$NetBSD: distinfo,v 1.2 2001/04/19 16:02:25 agc Exp $ +$NetBSD: distinfo,v 1.3 2004/08/16 23:58:35 ben Exp $ -SHA1 (phylip.tar.Z) = 1311d966d874faea7811611fe781b477d1e5228b -Size (phylip.tar.Z) = 932516 bytes +SHA1 (phylip-3.61.tar.gz) = f852d860cd2b05bfacb4c7b7ca9baa9163592106 +Size (phylip-3.61.tar.gz) = 835969 bytes +SHA1 (patch-aa) = c92bef99d88552d46a72ca8b2a4c8abb246537cd diff --git a/biology/phylip/patches/patch-aa b/biology/phylip/patches/patch-aa new file mode 100644 index 00000000000..2750e4f8290 --- /dev/null +++ b/biology/phylip/patches/patch-aa @@ -0,0 +1,13 @@ +$NetBSD: patch-aa,v 1.1 2004/08/16 23:58:35 ben Exp $ + +--- Makefile.orig 2004-08-15 12:23:29.000000000 +0200 ++++ Makefile 2004-08-15 12:24:04.000000000 +0200 +@@ -111,7 +111,7 @@ + # + # For gcc for Linux with X windows development packages installed + # or for MacOS X with X windows installed +-DLIBS= -L/usr/X11R6/lib/ -lX11 -lXaw -lXt ++DLIBS= -L/usr/X11R6/lib/ -Wl,-rpath,/usr/X11R6/lib -lX11 -lXaw -lXt + # + # 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