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

5 files changed, 104 insertions, 71 deletions

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
+ #
+ # ----------------------------------------------------------------------------
+ #