5 files changed, 30 insertions, 43 deletions

diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
index 50bed3da3219..68d49952b5a0 100644
--- a/biology/phylip/Makefile
+++ b/biology/phylip/Makefile
@@ -6,23 +6,22 @@
 #
 
 PORTNAME=	phylip
-PORTVERSION=	3.6
+PORTVERSION=	3.6.a2.1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/phylip/phylip36/
 DISTNAME=	${PORTNAME}
-WRKSRC=		${WRKDIR}/${DISTNAME}/src
 EXTRACT_SUFX=	.tar.Z
 
 MAINTAINER=	dbader@eece.unm.edu
 
 USE_XLIB=	yes
-NO_WRKSUBDIR=	yes
+BUILD_WRKSRC=	${WRKSRC}/src
 
 BINARIES=	clique consense contml contrast dnacomp dnadist dnainvar \
-		dnaml dnamlk dnamove dnapars dnapenny dolmove dollop \
+		dnaml dnamlk dnamove dnapars dnapenny dollop dolmove \
 		dolpenny drawgram drawtree factor fitch gendist kitsch \
-		mix move neighbor pars penny proml protdist protpars \
-		restdist restml retree seqboot treedist
+		mix move neighbor pars penny proml promlk protdist \
+		protpars restdist restml retree seqboot treedist
 DOCFILES=	clique.html consense.html contchar.html contml.html \
 		contrast.html discrete.html distance.html dnacomp.html \
 		dnadist.html dnainvar.html dnaml.html dnamlk.html \
@@ -30,19 +29,18 @@ DOCFILES=	clique.html consense.html contchar.html contml.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 proml.html protdist.html \
-		protpars.html restdist.html restml.html retree.html \
-		seqboot.html sequence.html treedist.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
 
 do-install:
 .for f in ${BINARIES}
-	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${f} ${PREFIX}/bin
 .endfor
 .if !defined(NOPORTDOCS)
-	${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
+	${MKDIR} ${DOCSDIR}
 .for f in ${DOCFILES}
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${f} \
-	${PREFIX}/share/doc/${PORTNAME}
+	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${f} ${DOCSDIR}
 .endfor
 .endif
 
diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo
index e67ac37b471f..1d66f6263f4f 100644
--- a/biology/phylip/distinfo
+++ b/biology/phylip/distinfo
@@ -1 +1 @@
-MD5 (phylip.tar.Z) = b705658b0de0163fe87b6416c521d98c
+MD5 (phylip.tar.Z) = c02517c689e3eeb974a6261b5fbe21bc
diff --git a/biology/phylip/files/patch-aa b/biology/phylip/files/patch-aa
index 78fbe0ed4f78..0d6ceae195fc 100644
--- a/biology/phylip/files/patch-aa
+++ b/biology/phylip/files/patch-aa
@@ -1,11 +1,20 @@
---- Makefile.orig	Mon Mar 26 19:31:01 2001
-+++ Makefile	Mon Mar 26 19:35:29 2001
-@@ -77,7 +77,7 @@
+--- src/Makefile.orig	Fri Aug 10 00:01:39 2001
++++ src/Makefile	Tue Aug 21 14:17:17 2001
+@@ -61,7 +61,7 @@
+ # Here are some possible CFLAGS statements:
+ #
+ # An optimized one
+-CFLAGS  = -O3 -fomit-frame-pointer
++CFLAGS += -O3 -fomit-frame-pointer
+ #
+ #A minimal one
+ #CFLAGS =
+@@ -83,7 +83,7 @@
  # and here are some possible DFLAGS statements:
  #
  # A minimal one
--DFLAGS  = -DX -lX11
-+DFLAGS  = -DX -I/usr/X11R6/include
+-DFLAGS  = -DX $(CFLAGS)
++DFLAGS  = -DX -I/usr/X11R6/include $(CFLAGS)
+ DLIBS= -lX11 -lXaw -lXt
  #
  # A basic one for debugging
- #DFLAGS  = -g -DX -lX11
diff --git a/biology/phylip/pkg-descr b/biology/phylip/pkg-descr
index 332989387f17..1e9171c8bc81 100644
--- a/biology/phylip/pkg-descr
+++ b/biology/phylip/pkg-descr
@@ -8,28 +8,6 @@ types that can be handled include molecular sequences, gene
 frequencies, restriction sites, distance matrices, and 0/1 discrete
 characters.
 
-The programs are controlled through a menu, which asks the users which
-options they want to set, and allows them to start the
-computation. The data are read into the program from a text file,
-which the user can prepare using any word processor or text editor
-(but it is important that this text file not be in the special format
-of that word processor -- it should instead be in "flat ASCII" or
-"Text Only" format). Some sequence analysis programs such as alignment
-programs can write data files in the PHYLIP format. Most of the
-programs look for the data in a file called "infile" -- if they do not
-find this file they then ask the user to type in the file name of the
-data file.
-
-Output is written onto special files with names like "outfile" and
-"treefile". Trees written onto "treefile" are in the Newick format, an
-informal standard agreed to in 1986 by authors of a number of major
-phylogeny packages.
-
-PHYLIP is the most widely-distributed phylogeny package, and competes
-with PAUP to be the one responsible for the largest number of
-published trees. PHYLIP has been in distribution since 1980, and has
-over 6,000 registered users.
-
  Joe Felsenstein
  joe@genetics.washington.edu
  Department of Genetics
@@ -37,4 +15,4 @@ over 6,000 registered users.
  Box 357360
  Seattle, Washington 98195-7360, U.S.A.
 
-WWW: http://evolution.genetics.washington.edu/phylip.html
\ No newline at end of file
+WWW: http://evolution.genetics.washington.edu/phylip.html
diff --git a/biology/phylip/pkg-plist b/biology/phylip/pkg-plist
index a16d24f04c39..5cc2e8cbd326 100644
--- a/biology/phylip/pkg-plist
+++ b/biology/phylip/pkg-plist
@@ -25,6 +25,7 @@ bin/neighbor
 bin/pars
 bin/penny
 bin/proml
+bin/promlk
 bin/protdist
 bin/protpars
 bin/restdist
@@ -65,6 +66,7 @@ bin/treedist
 %%PORTDOCS%%share/doc/phylip/penny.html
 %%PORTDOCS%%share/doc/phylip/phylip.gif
 %%PORTDOCS%%share/doc/phylip/proml.html
+%%PORTDOCS%%share/doc/phylip/promlk.html
 %%PORTDOCS%%share/doc/phylip/protdist.html
 %%PORTDOCS%%share/doc/phylip/protpars.html
 %%PORTDOCS%%share/doc/phylip/restdist.html