diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/phylip/Makefile | 23 | ||||
| -rw-r--r-- | biology/phylip/PLIST | 87 | ||||
| -rw-r--r-- | biology/phylip/distinfo | 10 | ||||
| -rw-r--r-- | biology/phylip/patches/patch-aa | 51 |
4 files changed, 89 insertions, 82 deletions
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile index f3e8caea082..690cac2c8ed 100644 --- a/biology/phylip/Makefile +++ b/biology/phylip/Makefile @@ -1,7 +1,6 @@ -# $NetBSD: Makefile,v 1.22 2009/05/19 08:59:04 wiz Exp $ +# $NetBSD: Makefile,v 1.23 2010/07/10 11:26:32 obache Exp $ -DISTNAME= phylip-3.61 -PKGREVISION= 3 +DISTNAME= phylip-3.69 CATEGORIES= biology MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ @@ -18,33 +17,33 @@ PKG_DESTDIR_SUPPORT= user-destdir WRKSRC= ${WRKDIR}/${DISTNAME}/src -INSTALLATION_DIRS= bin share/fonts/phylip share/doc/html/phylip +INSTALLATION_DIRS= bin share/fonts/phylip share/doc/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} \ - ${DESTDIR}${PREFIX}/share/doc/html/phylip + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${html} \ + ${DESTDIR}${PREFIX}/share/doc/phylip .endfor MAKE_ENV+= X11_LDFLAGS=${X11_LDFLAGS:Q} diff --git a/biology/phylip/PLIST b/biology/phylip/PLIST index 4389c487735..8afe0bade51 100644 --- a/biology/phylip/PLIST +++ b/biology/phylip/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.6 2009/06/14 18:11:08 joerg Exp $ +@comment $NetBSD: PLIST,v 1.7 2010/07/10 11:26:32 obache Exp $ bin/clique bin/consense bin/contml @@ -34,49 +34,48 @@ bin/restml bin/retree bin/seqboot bin/treedist -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 +share/doc/phylip/clique.html +share/doc/phylip/consense.html +share/doc/phylip/contchar.html +share/doc/phylip/contml.html +share/doc/phylip/contrast.html +share/doc/phylip/discrete.html +share/doc/phylip/distance.html +share/doc/phylip/dnacomp.html +share/doc/phylip/dnadist.html +share/doc/phylip/dnainvar.html +share/doc/phylip/dnaml.html +share/doc/phylip/dnamlk.html +share/doc/phylip/dnamove.html +share/doc/phylip/dnapars.html +share/doc/phylip/dnapenny.html +share/doc/phylip/dollop.html +share/doc/phylip/dolmove.html +share/doc/phylip/dolpenny.html +share/doc/phylip/draw.html +share/doc/phylip/drawgram.html +share/doc/phylip/drawtree.html +share/doc/phylip/factor.html +share/doc/phylip/fitch.html +share/doc/phylip/gendist.html +share/doc/phylip/kitsch.html +share/doc/phylip/main.html +share/doc/phylip/mix.html +share/doc/phylip/move.html +share/doc/phylip/neighbor.html +share/doc/phylip/pars.html +share/doc/phylip/penny.html +share/doc/phylip/phylip.gif +share/doc/phylip/proml.html +share/doc/phylip/promlk.html +share/doc/phylip/protdist.html +share/doc/phylip/protpars.html +share/doc/phylip/restdist.html +share/doc/phylip/restml.html +share/doc/phylip/retree.html +share/doc/phylip/seqboot.html +share/doc/phylip/sequence.html +share/doc/phylip/treedist.html share/fonts/phylip/font1 share/fonts/phylip/font2 share/fonts/phylip/font3 diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo index f274d845d07..41c03d12905 100644 --- a/biology/phylip/distinfo +++ b/biology/phylip/distinfo @@ -1,6 +1,6 @@ -$NetBSD: distinfo,v 1.5 2005/12/28 13:46:07 joerg Exp $ +$NetBSD: distinfo,v 1.6 2010/07/10 11:26:32 obache 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) = 2439ca6348fe29a534f8e305cbe4ff5e66ee3c03 diff --git a/biology/phylip/patches/patch-aa b/biology/phylip/patches/patch-aa index 608ac7ad8c3..7d55dfe7c4f 100644 --- a/biology/phylip/patches/patch-aa +++ b/biology/phylip/patches/patch-aa @@ -1,31 +1,40 @@ -$NetBSD: patch-aa,v 1.2 2005/12/28 13:46:07 joerg Exp $ +$NetBSD: patch-aa,v 1.3 2010/07/10 11:26:32 obache Exp $ ---- Makefile.orig 2003-12-23 05:21:14.000000000 +0000 +--- Makefile.orig 2009-09-08 22:14:56.000000000 +0000 +++ Makefile -@@ -62,7 +62,7 @@ EXEDIR = ../exe +@@ -78,7 +78,7 @@ EXEDIR = ../exe + # The next two assignments are the invocations of the compiler # + # This one specifies the "cc" C compiler +-CC = cc ++#CC = cc # - #A minimal one --CFLAGS = -+#CFLAGS = - # - # A basic one for debugging + # To use GCC instead: + #CC = gcc +@@ -97,7 +97,7 @@ 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 # -@@ -119,7 +119,7 @@ DLIBS= -L/usr/X11R6/lib/ -lX11 -lXaw -lX - # ordinary compiles and the tree-drawing programs, CC and DC +@@ -128,7 +128,7 @@ CFLAGS = -O3 -fomit-frame-pointer + # use the corresponding value for $(DLIBS). If the Xlib library + # for the X windowing system is somewhere unexpected, you may have + # to change the path /usr/X11R6/lib in this one. +-DFLAGS = $(CFLAGS) -DX -I/usr/X11R6/include ++DFLAGS = $(CFLAGS) -DX -I${X11BASE}/include # - # This one specifies the "cc" C compiler --CC = cc $(CFLAGS) -+CC := ${CC} $(CFLAGS) + # ---------------------------------------------------------------------------- + # +@@ -149,7 +149,7 @@ 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 # - # 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) |