[pkgsrc/trunk]: pkgsrc/biology/phylip Update phylip to version 3.61. No Chan...

[ben <ben%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/28043e0c56bd
branches:  trunk
changeset: 479559:28043e0c56bd
user:      ben <ben%pkgsrc.org@localhost>
date:      Mon Aug 16 23:58:35 2004 +0000

description:
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

diffstat:

 biology/phylip/DESCR            |    5 +-
 biology/phylip/Makefile         |   46 ++++++++-----
 biology/phylip/PLIST            |  128 +++++++++++++++++++++------------------
 biology/phylip/distinfo         |    7 +-
 biology/phylip/patches/patch-aa |   13 ++++
 5 files changed, 116 insertions(+), 83 deletions(-)

diffs (255 lines):

diff -r 1f5895bef1e0 -r 28043e0c56bd biology/phylip/DESCR
--- a/biology/phylip/DESCR      Mon Aug 16 23:46:57 2004 +0000
+++ b/biology/phylip/DESCR      Mon Aug 16 23:58:35 2004 +0000
@@ -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 -r 1f5895bef1e0 -r 28043e0c56bd biology/phylip/Makefile
--- a/biology/phylip/Makefile   Mon Aug 16 23:46:57 2004 +0000
+++ b/biology/phylip/Makefile   Mon Aug 16 23:58:35 2004 +0000
@@ -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@localhost
 HOMEPAGE=      http://evolution.genetics.washington.edu/phylip.html
@@ -15,25 +12,36 @@
 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/fonts/phylip
+.for FONT in font1 font2 font3 font4 font5 font6
+       ${INSTALL_DATA} ${WRKSRC}/${FONT} ${PREFIX}/share/fonts/phylip
 .endfor
-       ${INSTALL_DATA_DIR} ${PREFIX}/share/misc/phylip
-.for FONT in font1 font2 font3 font4 font5 font6
-       ${INSTALL_DATA} ${WRKSRC}/${FONT} ${PREFIX}/share/misc/phylip
+       ${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 -r 1f5895bef1e0 -r 28043e0c56bd biology/phylip/PLIST
--- a/biology/phylip/PLIST      Mon Aug 16 23:46:57 2004 +0000
+++ b/biology/phylip/PLIST      Mon Aug 16 23:58:35 2004 +0000
@@ -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/factor
+bin/fitch
+bin/gendist
+bin/kitsch
+bin/mix
+bin/move
+bin/neighbor
+bin/pars
+bin/penny
+bin/proml
+bin/promlk
+bin/protdist
+bin/protpars
+bin/restdist
+bin/restml
+bin/retree
+bin/seqboot
+bin/treedist
 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/penny
-share/doc/phylip/penny.doc
-bin/protdist
-share/doc/phylip/protdist.doc
-bin/protpars
-share/doc/phylip/protpars.doc
-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
+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 -r 1f5895bef1e0 -r 28043e0c56bd biology/phylip/distinfo
--- a/biology/phylip/distinfo   Mon Aug 16 23:46:57 2004 +0000
+++ b/biology/phylip/distinfo   Mon Aug 16 23:58:35 2004 +0000
@@ -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 -r 1f5895bef1e0 -r 28043e0c56bd biology/phylip/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/phylip/patches/patch-aa   Mon Aug 16 23:58:35 2004 +0000
@@ -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
+ #
+ # ----------------------------------------------------------------------------
+ #