From owner-freebsd-ports-bugs@FreeBSD.ORG Mon Jan 23 05:00:28 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 56F0116A41F for ; Mon, 23 Jan 2006 05:00:28 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 9C24F43D5E for ; Mon, 23 Jan 2006 05:00:20 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k0N50KUn063372 for ; Mon, 23 Jan 2006 05:00:20 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k0N50KMF063371; Mon, 23 Jan 2006 05:00:20 GMT (envelope-from gnats) Resent-Date: Mon, 23 Jan 2006 05:00:20 GMT Resent-Message-Id: <200601230500.k0N50KMF063371@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, "Choe, Cheng-Dae" Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 21A6516A41F for ; Mon, 23 Jan 2006 04:57:47 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [216.136.204.117]) by mx1.FreeBSD.org (Postfix) with ESMTP id D64D443D45 for ; Mon, 23 Jan 2006 04:57:46 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.13.1/8.13.1) with ESMTP id k0N4vkNr062485 for ; Mon, 23 Jan 2006 04:57:46 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.13.1/8.13.1/Submit) id k0N4vkjo062484; Mon, 23 Jan 2006 04:57:46 GMT (envelope-from nobody) Message-Id: <200601230457.k0N4vkjo062484@www.freebsd.org> Date: Mon, 23 Jan 2006 04:57:46 GMT From: "Choe, Cheng-Dae" To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-2.3 Cc: Subject: ports/92182: update biology/phylip to 3.65 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 23 Jan 2006 05:00:28 -0000 >Number: 92182 >Category: ports >Synopsis: update biology/phylip to 3.65 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Jan 23 05:00:19 GMT 2006 >Closed-Date: >Last-Modified: >Originator: "Choe, Cheng-Dae" >Release: FreeBSD 6.0-STABLE i386 >Organization: >Environment: System: FreeBSD w.comdongin.com 6.0-STABLE FreeBSD 6.0-STABLE #1: Sat Jan 21 00:34:59 KST 2006 root@w.comdongin.com:/usr/obj/data/src/sys/CDI i386 >Description: - update phylip to 3.65 - use Makefile's PORTDOCS variables - install documents in post-install target - installed files are not listed in Makefile(more flexible), find and installed with ${FIND} command >How-To-Repeat: N/A >Fix: diff -ruN phylip.orig/Makefile phylip/Makefile --- phylip.orig/Makefile Fri Apr 22 21:08:12 2005 +++ phylip/Makefile Mon Jan 23 11:19:33 2006 @@ -6,8 +6,7 @@ # PORTNAME= phylip -PORTVERSION= 3.6 -PORTEPOCH= 1 +PORTVERSION= 3.65 CATEGORIES= biology MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ \ http://bioinformatics.weizmann.ac.il/software/linkage_and_mapping/phylip/ \ @@ -17,6 +16,7 @@ MAINTAINER= dbader@ece.unm.edu COMMENT= A Phylogeny Inference Package +WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} USE_XLIB= yes BUILD_WRKSRC= ${WRKSRC}/src @@ -24,36 +24,23 @@ DC="${CC} -DX -I${X11BASE}/include ${CFLAGS}" \ GLIBS="-L${X11BASE}/lib -lX11 -lm" -BINARIES= clique consense contml contrast dnacomp dnadist dnainvar \ - dnaml dnamlk dnamove dnapars dnapenny dollop dolmove \ - dolpenny drawgram drawtree factor fitch gendist kitsch \ - 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 \ - 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 proml.html promlk.html \ - protdist.html protpars.html restdist.html restml.html \ - retree.html seqboot.html sequence.html treedist.html -FONTFILES= font1 font2 font3 font4 font5 font6 +PORTDOCS= * do-install: -.for f in ${BINARIES} - ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${f} ${PREFIX}/bin -.endfor + @cd ${BUILD_WRKSRC} && ${MAKE} install + + @cd ${WRKSRC}/exe && \ + ${FIND} . -not -type d -not -name 'font*' -exec ${INSTALL_PROGRAM} "{}" "${PREFIX}/bin/{}" \; + ${MKDIR} ${DATADIR} -.for font in ${FONTFILES} - ${INSTALL_DATA} ${BUILD_WRKSRC}/${font} ${DATADIR} -.endfor + @cd ${WRKSRC}/exe && \ + ${FIND} . -not -type d -name 'font*' -exec ${INSTALL_DATA} "{}" "${DATADIR}/{}" \; + +post-install: .if !defined(NOPORTDOCS) ${MKDIR} ${DOCSDIR} -.for f in ${DOCFILES} - ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${f} ${DOCSDIR} -.endfor + @cd ${WRKSRC}/doc && \ + ${FIND} . -not -type d -exec ${INSTALL_DATA} "{}" "${DOCSDIR}/{}" \; .endif .include diff -ruN phylip.orig/distinfo phylip/distinfo --- phylip.orig/distinfo Mon Jan 23 03:09:06 2006 +++ phylip/distinfo Mon Jan 23 09:24:24 2006 @@ -1,3 +1,3 @@ -MD5 (phylip-3.6.tar.gz) = ff0ded7756db29d948f355ed5cc020cc -SHA256 (phylip-3.6.tar.gz) = 2e5ccf074ae33d17302afc75dd0533a189502bb2b83ed361ccc345cad09a142b -SIZE (phylip-3.6.tar.gz) = 855538 +MD5 (phylip-3.65.tar.gz) = c89a92c8692faaba4310b69b2d89bc33 +SHA256 (phylip-3.65.tar.gz) = 8f8ab66a58dbe1fdf0b615c13b6d358d6c49195fbaeaabc6190253e895c0d528 +SIZE (phylip-3.65.tar.gz) = 1036976 diff -ruN phylip.orig/pkg-plist phylip/pkg-plist --- phylip.orig/pkg-plist Tue Oct 12 07:26:34 2004 +++ phylip/pkg-plist Mon Jan 23 13:19:21 2006 @@ -33,48 +33,6 @@ bin/retree bin/seqboot bin/treedist -%%PORTDOCS%%%%DOCSDIR%%/clique.html -%%PORTDOCS%%%%DOCSDIR%%/consense.html -%%PORTDOCS%%%%DOCSDIR%%/contchar.html -%%PORTDOCS%%%%DOCSDIR%%/contml.html -%%PORTDOCS%%%%DOCSDIR%%/contrast.html -%%PORTDOCS%%%%DOCSDIR%%/discrete.html -%%PORTDOCS%%%%DOCSDIR%%/distance.html -%%PORTDOCS%%%%DOCSDIR%%/dnacomp.html -%%PORTDOCS%%%%DOCSDIR%%/dnadist.html -%%PORTDOCS%%%%DOCSDIR%%/dnainvar.html -%%PORTDOCS%%%%DOCSDIR%%/dnaml.html -%%PORTDOCS%%%%DOCSDIR%%/dnamlk.html -%%PORTDOCS%%%%DOCSDIR%%/dnamove.html -%%PORTDOCS%%%%DOCSDIR%%/dnapars.html -%%PORTDOCS%%%%DOCSDIR%%/dnapenny.html -%%PORTDOCS%%%%DOCSDIR%%/dollop.html -%%PORTDOCS%%%%DOCSDIR%%/dolmove.html -%%PORTDOCS%%%%DOCSDIR%%/dolpenny.html -%%PORTDOCS%%%%DOCSDIR%%/draw.html -%%PORTDOCS%%%%DOCSDIR%%/drawgram.html -%%PORTDOCS%%%%DOCSDIR%%/drawtree.html -%%PORTDOCS%%%%DOCSDIR%%/factor.html -%%PORTDOCS%%%%DOCSDIR%%/fitch.html -%%PORTDOCS%%%%DOCSDIR%%/gendist.html -%%PORTDOCS%%%%DOCSDIR%%/kitsch.html -%%PORTDOCS%%%%DOCSDIR%%/main.html -%%PORTDOCS%%%%DOCSDIR%%/mix.html -%%PORTDOCS%%%%DOCSDIR%%/move.html -%%PORTDOCS%%%%DOCSDIR%%/neighbor.html -%%PORTDOCS%%%%DOCSDIR%%/pars.html -%%PORTDOCS%%%%DOCSDIR%%/penny.html -%%PORTDOCS%%%%DOCSDIR%%/phylip.gif -%%PORTDOCS%%%%DOCSDIR%%/proml.html -%%PORTDOCS%%%%DOCSDIR%%/promlk.html -%%PORTDOCS%%%%DOCSDIR%%/protdist.html -%%PORTDOCS%%%%DOCSDIR%%/protpars.html -%%PORTDOCS%%%%DOCSDIR%%/restdist.html -%%PORTDOCS%%%%DOCSDIR%%/restml.html -%%PORTDOCS%%%%DOCSDIR%%/retree.html -%%PORTDOCS%%%%DOCSDIR%%/seqboot.html -%%PORTDOCS%%%%DOCSDIR%%/sequence.html -%%PORTDOCS%%%%DOCSDIR%%/treedist.html %%DATADIR%%/font1 %%DATADIR%%/font2 %%DATADIR%%/font3 @@ -82,4 +40,3 @@ %%DATADIR%%/font5 %%DATADIR%%/font6 @dirrm %%DATADIR%% -%%PORTDOCS%%@dirrm %%DOCSDIR%% >Release-Note: >Audit-Trail: >Unformatted: