From owner-freebsd-ports-bugs@FreeBSD.ORG Thu Oct 28 18:20:27 2004 Return-Path: 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 9E97716A4CE for ; Thu, 28 Oct 2004 18:20:27 +0000 (GMT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 3F60943D66 for ; Thu, 28 Oct 2004 18:20:05 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) i9SIK5iC096282 for ; Thu, 28 Oct 2004 18:20:05 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.11/8.12.11/Submit) id i9SIK51g096281; Thu, 28 Oct 2004 18:20:05 GMT (envelope-from gnats) Resent-Date: Thu, 28 Oct 2004 18:20:05 GMT Resent-Message-Id: <200410281820.i9SIK51g096281@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 4624516A4CE for ; Thu, 28 Oct 2004 18:15:53 +0000 (GMT) Received: from www.freebsd.org (www.freebsd.org [216.136.204.117]) by mx1.FreeBSD.org (Postfix) with ESMTP id 13B3D43D67 for ; Thu, 28 Oct 2004 18:15:53 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.12.11/8.12.11) with ESMTP id i9SIFqqC043378 for ; Thu, 28 Oct 2004 18:15:52 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.12.11/8.12.11/Submit) id i9SIFqee043372; Thu, 28 Oct 2004 18:15:52 GMT (envelope-from nobody) Message-Id: <200410281815.i9SIFqee043372@www.freebsd.org> Date: Thu, 28 Oct 2004 18:15:52 GMT From: "Choe, Cheng-Dae" To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-2.3 Subject: ports/73250: update biology/hmmer to 2.3.2 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 28 Oct 2004 18:20:27 -0000 >Number: 73250 >Category: ports >Synopsis: update biology/hmmer to 2.3.2 >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu Oct 28 18:20:04 GMT 2004 >Closed-Date: >Last-Modified: >Originator: "Choe, Cheng-Dae" >Release: FreeBSD 5.3-STABLE i386 >Organization: >Environment: System: FreeBSD comdongin.com 5.3-STABLE FreeBSD 5.3-STABLE #0: Thu Oct 21 09:48:27 KST 2004 root@comdongin.com:/usr/obj/data/src/sys/CDI i386 >Description: update biology/hmmer to 2.3.2 >How-To-Repeat: N/A >Fix: diff -ruN hmmer.orig/Makefile hmmer/Makefile --- hmmer.orig/Makefile Fri Oct 29 00:59:26 2004 +++ hmmer/Makefile Fri Oct 29 01:52:53 2004 @@ -6,24 +6,22 @@ # PORTNAME= hmmer -PORTVERSION= 2.2.g -PORTREVISION= 1 +PORTVERSION= 2.3.2 +PORTREVISION= 0 CATEGORIES= biology -MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${VERSIONSTRING}/ -DISTNAME= ${PORTNAME}-${VERSIONSTRING} +MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${PORTVERSION}/ +DISTNAME= ${PORTNAME}-${PORTVERSION} MAINTAINER= wjv@FreeBSD.org COMMENT= Profile hidden Markov models for biological sequence analysis GNU_CONFIGURE= yes USE_PERL5= yes -VERSIONSTRING= ${PORTVERSION:C|\.([^.]*)$|\1|} DOCFILES= 00README COPYRIGHT NOTES Userguide.pdf -MAN1= afetch.1 alistat.1 hmmalign.1 hmmbuild.1 hmmcalibrate.1 \ - hmmconvert.1 hmmemit.1 hmmer.1 hmmfetch.1 hmmindex.1 \ - hmmpfam.1 hmmsearch.1 seqstat.1 sfetch.1 shuffle.1 \ - sreformat.1 + +MAN1= hmmalign.1 hmmcalibrate.1 hmmemit.1 hmmfetch.1 hmmpfam.1 \ + hmmbuild.1 hmmconvert.1 hmmer.1 hmmindex.1 hmmsearch.1 post-install: .if !defined(NOPORTDOCS) diff -ruN hmmer.orig/distinfo hmmer/distinfo --- hmmer.orig/distinfo Fri Oct 29 00:59:26 2004 +++ hmmer/distinfo Fri Oct 29 01:06:00 2004 @@ -1,2 +1,2 @@ -MD5 (hmmer-2.2g.tar.gz) = d7def2007a0aaf2eafb9a96a07986b8c -SIZE (hmmer-2.2g.tar.gz) = 931569 +MD5 (hmmer-2.3.2.tar.gz) = 5f073340c0cf761288f961a73821228a +SIZE (hmmer-2.3.2.tar.gz) = 1024933 diff -ruN hmmer.orig/files/patch-Makefile.in hmmer/files/patch-Makefile.in --- hmmer.orig/files/patch-Makefile.in Fri Oct 29 00:59:26 2004 +++ hmmer/files/patch-Makefile.in Fri Oct 29 02:55:45 2004 @@ -1,27 +1,28 @@ ---- Makefile.in.orig Mon Aug 6 01:55:36 2001 -+++ Makefile.in Wed Aug 22 14:52:30 2001 + +$FreeBSD$ + +--- Makefile.in.orig ++++ Makefile.in @@ -34,7 +34,7 @@ # how to install the man pages; # cp is generally fine, unless you preformat your pages. # -INSTMAN = cp -+INSTMAN = $(BSD_INSTALL_MAN) ++INSTMAN = ${INSTALL} MANSUFFIX = 1 # your compiler and compiler flags -@@ -144,12 +144,12 @@ +@@ -109,10 +109,12 @@ # installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1) + # Creates these directories if they don't exist. install: - for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\ -- cp binaries/$$file $(BINDIR)/;\ -+ $(BSD_INSTALL_PROGRAM) binaries/$$file $(BINDIR)/;\ ++ (cd squid; make install) ++ + mkdir -p ${BINDIR} + -mkdir -p ${MANDIR}/man${MANSUFFIX} + for file in $(PROGS) $(PVMPROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ ${INSTALL} src/$$file $(BINDIR)/;\ done -- for file in hmmer $(PROGS) $(SQUIDPROGS); do\ -+ for file in hmmer $(PROGS); do\ + -for file in hmmer $(PROGS); do\ $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ - done -- for file in $(SQUIDPROGS); do\ -+ for file in afetch alistat seqstat sfetch shuffle sreformat; do\ - $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ - done - diff -ruN hmmer.orig/files/patch-configure hmmer/files/patch-configure --- hmmer.orig/files/patch-configure Fri Oct 29 00:59:26 2004 +++ hmmer/files/patch-configure Thu Jan 1 09:00:00 1970 @@ -1,22 +0,0 @@ ---- configure.orig Mon Aug 6 01:55:52 2001 -+++ configure Thu Jul 11 12:38:47 2002 -@@ -1094,6 +1094,9 @@ - - acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags" - ;; -+ *freebsd5*) -+ acx_pthread_flags="-lc_r -kthread lthread -pthread" -+ ;; - esac - - if test x"$acx_pthread_ok" = xno; then -@@ -1418,6 +1421,9 @@ - # we'll just look for -pthreads and -lpthread first: - - acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags" -+ ;; -+ *freebsd5*) -+ acx_pthread_flags="-lc_r -kthread lthread -pthread" - ;; - esac - diff -ruN hmmer.orig/files/patch-squid_Makefile.in hmmer/files/patch-squid_Makefile.in --- hmmer.orig/files/patch-squid_Makefile.in Thu Jan 1 09:00:00 1970 +++ hmmer/files/patch-squid_Makefile.in Fri Oct 29 02:55:47 2004 @@ -0,0 +1,30 @@ + +$FreeBSD$ + +--- squid/Makefile.in.orig ++++ squid/Makefile.in +@@ -177,16 +177,17 @@ + test -d $(SCRIPTDIR) || mkdir -p $(SCRIPTDIR) + test -d $(INCLUDEDIR)|| mkdir -p $(INCLUDEDIR) + test -d $(MANDIR)/man$(MANSUFFIX) || mkdir -p $(MANDIR)/man$(MANSUFFIX) +- cp libsquid.a $(LIBDIR)/ +- cp $(HDRS) $(INCLUDEDIR)/ +- cp $(POSTCONFHDRS) $(INCLUDEDIR)/ +- cp $(PROGS) $(BINDIR)/ ++ ${INSTALL} libsquid.a $(LIBDIR)/ ++ ${INSTALL} $(HDRS) $(INCLUDEDIR)/ ++ ${INSTALL} $(POSTCONFHDRS) $(INCLUDEDIR)/ ++ ${INSTALL} $(PROGS) $(BINDIR)/ ++# Hmmer packages has no script and manpages + # for scriptfile in $(SCRIPTS); do\ + # cp Scripts/$$scriptfile $(SCRIPTDIR)/;\ + # done +- @for manpage in $(MANS); do\ +- $(INSTMAN) Man/$$manpage.man $(MANDIR)/man$(MANSUFFIX)/$$manpage.$(MANSUFFIX);\ +- done ++# @for manpage in $(MANS); do\ ++# $(INSTMAN) Man/$$manpage.man $(MANDIR)/man$(MANSUFFIX)/$$manpage.$(MANSUFFIX);\ ++# done + + uninstall: + rm $(LIBDIR)/libsquid.a diff -ruN hmmer.orig/pkg-plist hmmer/pkg-plist --- hmmer.orig/pkg-plist Fri Oct 29 00:59:26 2004 +++ hmmer/pkg-plist Fri Oct 29 02:30:08 2004 @@ -1,5 +1,7 @@ bin/afetch bin/alistat +bin/compalign +bin/compstruct bin/hmmalign bin/hmmbuild bin/hmmcalibrate @@ -9,11 +11,27 @@ bin/hmmindex bin/hmmpfam bin/hmmsearch +bin/revcomp +bin/seqsplit bin/seqstat bin/sfetch bin/shuffle bin/sindex bin/sreformat +bin/translate +bin/weight +include/gki.h +include/gsi.h +include/msa.h +include/rk.h +include/sqfuncs.h +include/squid.h +include/squidconf.h +include/sre_random.h +include/ssi.h +include/stopwatch.h +include/vectorops.h +lib/libsquid.a %%PORTDOCS%%%%DOCSDIR%%/00README %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT %%PORTDOCS%%%%DOCSDIR%%/NOTES >Release-Note: >Audit-Trail: >Unformatted: