pkg/43388: [biology/phylip] Update to 3.69

[wenheping%gmail.com@localhost]

>Number:         43388
>Category:       pkg
>Synopsis:       [biology/phylip] Update to 3.69
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    pkg-manager
>State:          open
>Class:          change-request
>Submitter-Id:   net
>Arrival-Date:   Sun May 30 04:10:01 +0000 2010
>Originator:     Wen Heping
>Release:        NetBSD-5.0.2
>Organization:
Private
>Environment:
NetBSD nb502.wenjing.com 5.0.2 NetBSD 5.0.2 (GENERIC) #0: Sat Feb  6 17:53:27 
UTC 2010  
builds%b7.netbsd.org@localhost:/home/builds/ab/netbsd-5-0-2-RELEASE/i386/201002061851Z-obj/home/builds/ab/netbsd-5-0-2-RELEASE/src/sys/arch/i386/compile/GENERIC
 i386
>Description:
Please visit:

http://evolution.gs.washington.edu/phylip/bugs.html
>How-To-Repeat:

>Fix:
diff -urN -x CVS phylip/Makefile phylip.new/Makefile
--- phylip/Makefile     2009-05-19 16:59:04.000000000 +0800
+++ phylip.new/Makefile 2010-05-30 19:54:04.000000000 +0800
@@ -1,7 +1,6 @@
 # $NetBSD: Makefile,v 1.22 2009/05/19 08:59:04 wiz Exp $

-DISTNAME=      phylip-3.61
-PKGREVISION=   3
+DISTNAME=      phylip-3.69
 CATEGORIES=    biology
 MASTER_SITES=  ftp://evolution.genetics.washington.edu/pub/phylip/

@@ -21,29 +20,29 @@
 INSTALLATION_DIRS=     bin share/fonts/phylip share/doc/html/phylip

 do-install:
-.for PROGRAM in clique consense contml contrast dnacomp dnadist                
\
+.for prog in clique consense contml contrast dnacomp dnadist           \
                dnainvar dnaml dnamlk dnamove dnapars dnapenny          \
                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} ${DESTDIR}${PREFIX}/bin
+       ${INSTALL_PROGRAM} ${WRKSRC}/${prog} ${DESTDIR}${PREFIX}/bin
 .endfor
-.for FONT in font1 font2 font3 font4 font5 font6
-       ${INSTALL_DATA} ${WRKSRC}/${FONT} ${DESTDIR}${PREFIX}/share/fonts/phylip
+.for font in font1 font2 font3 font4 font5 font6
+       ${INSTALL_DATA} ${WRKSRC}/${font} ${DESTDIR}${PREFIX}/share/fonts/phylip
 .endfor
-.for HTML in clique.html consense.html contchar.html contml.html       \
+.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  \
+               pars.html penny.html phylip.gif 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}               \
+       ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${html}               \
                ${DESTDIR}${PREFIX}/share/doc/html/phylip
 .endfor

diff -urN -x CVS phylip/PLIST phylip.new/PLIST
--- phylip/PLIST        2009-06-15 02:11:08.000000000 +0800
+++ phylip.new/PLIST    2010-05-30 04:10:35.000000000 +0800
@@ -66,7 +66,6 @@
 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
diff -urN -x CVS phylip/distinfo phylip.new/distinfo
--- phylip/distinfo     2005-12-28 21:46:07.000000000 +0800
+++ phylip.new/distinfo 2010-05-30 19:56:02.000000000 +0800
@@ -1,6 +1,6 @@
 $NetBSD: distinfo,v 1.5 2005/12/28 13:46:07 joerg Exp $

-SHA1 (phylip-3.61.tar.gz) = f852d860cd2b05bfacb4c7b7ca9baa9163592106
-RMD160 (phylip-3.61.tar.gz) = c783f947f204a653d9d5ed8e54e93368c46513de
-Size (phylip-3.61.tar.gz) = 835969 bytes
-SHA1 (patch-aa) = 268469d311183447d86db0274f0fd5079c6b16d6
+SHA1 (phylip-3.69.tar.gz) = ada364d1a588935ff59a23c08337d9dd99109c5e
+RMD160 (phylip-3.69.tar.gz) = a39080b959452957576c9b7daa2b9e7f25bef212
+Size (phylip-3.69.tar.gz) = 1511935 bytes
+SHA1 (patch-aa) = 4f833d7777e97b2d872930577fb4283eb597a6ba
diff -urN -x CVS phylip/patches/patch-aa phylip.new/patches/patch-aa
--- phylip/patches/patch-aa     2005-12-28 21:46:07.000000000 +0800
+++ phylip.new/patches/patch-aa 2010-05-30 04:03:48.000000000 +0800
@@ -1,31 +1,32 @@
-$NetBSD: patch-aa,v 1.2 2005/12/28 13:46:07 joerg Exp $
+$NetBSD$

---- Makefile.orig      2003-12-23 05:21:14.000000000 +0000
+--- Makefile.orig      2010-05-29 19:22:59.000000000 +0000
 +++ Makefile
-@@ -62,7 +62,7 @@ EXEDIR  = ../exe
+@@ -78,7 +78,8 @@ EXEDIR  = ../exe
+ # The next two assignments are the invocations of the compiler
  #
- #
- #A minimal one
--CFLAGS =
-+#CFLAGS =
- #
- # A basic one for debugging
+ # This one specifies the "cc" C compiler
+-CC        = cc
++# CC        = cc
++CC := ${CC} $(CFLAGS)
+ #
+ #  To use GCC instead:
+ #CC        = gcc
+@@ -97,7 +98,7 @@ CC        = cc
  #CFLAGS  = -g
-@@ -111,7 +111,7 @@ LIBS    = -lm
  #
- # 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= ${X11_LDFLAGS} -lX11 -lXaw -lXt
+ # An optimized one for gcc
+-CFLAGS  = -O3 -fomit-frame-pointer
++# CFLAGS  = -O3 -fomit-frame-pointer
+ #
+ # For some serious debugging using Gnu gcc
+ #
+@@ -149,7 +150,7 @@ LIBS    = -lm
+ # to change the path /usr/X11R6/lib in this one. If you use this
+ # value for $(DLIBS), you should also use the corresponding value
+ # for $(DFLAGS)
+-DLIBS= $(LIBS) -L/usr/X11R6/lib/ -lX11 -lXaw -lXt
++DLIBS= $(LIBS) ${X11_LDFLAGS} -lX11 -lXaw -lXt
  #
  # ----------------------------------------------------------------------------
- #
-@@ -119,7 +119,7 @@ DLIBS= -L/usr/X11R6/lib/ -lX11 -lXaw -lX
- # ordinary compiles and the tree-drawing programs, CC and DC
- #
- # This one specifies the "cc" C compiler
--CC        = cc $(CFLAGS)
-+CC        := ${CC} $(CFLAGS)
- #
- #  To use GCC instead, if it is not the compiler that "cc" invokes
- #CC        = gcc $(CFLAGS)
+ #  (After this point there should not be any reason to change anything)