From owner-freebsd-ports-bugs@FreeBSD.ORG Tue Oct 26 07:17:41 2004 Return-Path: Delivered-To: freebsd-ports-bugs@freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 7700E16A4CF for ; Tue, 26 Oct 2004 07:17:41 +0000 (GMT) Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.198]) by mx1.FreeBSD.org (Postfix) with ESMTP id E6A7643D31 for ; Tue, 26 Oct 2004 07:17:40 +0000 (GMT) (envelope-from whitekid@gmail.com) Received: by wproxy.gmail.com with SMTP id 68so135649wri for ; Tue, 26 Oct 2004 00:17:40 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:references; b=MOG7WqiVG11yqItTu/+6w6h1B8s8NQG6XHXoLAmJyfkrm9frTMblxK9gWCK8wLuPET65BkmDotqGwalxtDYRbyiAxJVr5Xm2SB7/1gilX1lexBEeenZXYYSD7+l317tPq7h++rg1N/iprsEUysZF35L3qp/iJyqaaiLe2VKxiSQ= Received: by 10.38.65.59 with SMTP id n59mr291402rna; Tue, 26 Oct 2004 00:17:40 -0700 (PDT) Received: by 10.38.96.4 with HTTP; Tue, 26 Oct 2004 00:17:40 -0700 (PDT) Message-ID: <38c00bae04102600171ba376c2@mail.gmail.com> Date: Tue, 26 Oct 2004 16:17:40 +0900 From: "Choe, Cheng-Dae" To: freebsd-gnats-submit@freebsd.org, freebsd-ports-bugs@freebsd.org In-Reply-To: <38c00bae04102523527c4717d0@mail.gmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit References: <200410260646.i9Q6kHEd040608@www.freebsd.org> <200410260650.i9Q6oPeo022018@freefall.freebsd.org> <38c00bae04102523527c4717d0@mail.gmail.com> Subject: Re: ports/73149: [New ports]: biology/mpiblast X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list Reply-To: "Choe, Cheng-Dae" List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 26 Oct 2004 07:17:41 -0000 Sorry again. I missed patch (files/*) again. Here is the REALLY correct pr for biology/mpiblast. I so sorry... ---------------------------- # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # mpiblast # mpiblast/Makefile # mpiblast/distinfo # mpiblast/pkg-descr # mpiblast/pkg-message # mpiblast/pkg-plist # mpiblast/files # mpiblast/files/patch-src_Makefile.in # mpiblast/files/patch-src_Makefile.am # echo c - mpiblast mkdir -p mpiblast > /dev/null 2>&1 echo x - mpiblast/Makefile sed 's/^X//' >mpiblast/Makefile << 'END-of-mpiblast/Makefile' X# New ports collection makefile for: mpiblast X# Date created: 23 October 2004 X# Whom: whitekid X# X# $FreeBSD$ X# X XPORTNAME= mpiblast XPORTVERSION= 1.2.1 XPORTREVISION= 0 XCATEGORIES= biology parallel XMASTER_SITES= http://mpiblast.lanl.gov/releases/ XDISTNAME= mpiBLAST-${PORTVERSION} X XMAINTAINER= whitekid@gmail.com XCOMMENT= A parallelization for NCBI BLAST X XBUILD_DEPENDS= ${NONEXISTENT}:${PORTSDIR}/biology/ncbi-toolkit:build \ X ${LOCALBASE}/include/mpi.h:${PORTSDIR}/net/lam X XGNU_CONFIGURE= yes X XCONFIGURE_ARGS= --with-ncbi=${PORTSDIR}/biology/ncbi-toolkit/work/ncbi X XDOCS= AUTHORS COPYING ChangeLog INSTALL LICENSE NEWS README TODO XDATAS= WWWBlastWrap.pl X Xpost-install: X @${INSTALL_DATA} ${WRKSRC}/mpiblast.conf ${PREFIX}/etc/mpiblast.conf.sample X X.if !defined(NOPORTDOCS) X @${MKDIR} ${DOCSDIR} X.for file in ${DOCS} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DOCSDIR} X.endfor X X @${MKDIR} ${DATADIR} X.for file in ${DATAS} X @${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR} X.endfor X.endif X X.include END-of-mpiblast/Makefile echo x - mpiblast/distinfo sed 's/^X//' >mpiblast/distinfo << 'END-of-mpiblast/distinfo' XMD5 (mpiBLAST-1.2.1.tar.gz) = 7724f4fbdcecd00d0cc597214efd54e1 XSIZE (mpiBLAST-1.2.1.tar.gz) = 170513 END-of-mpiblast/distinfo echo x - mpiblast/pkg-descr sed 's/^X//' >mpiblast/pkg-descr << 'END-of-mpiblast/pkg-descr' XmpiBLAST is a freely available open source parallelization of NCBI BLAST. XmpiBLAST segments the BLAST database and distributes it across cluster nodes, Xpermitting BLAST queries to be processed on many nodes simultaneously. mpiBLAST Xis based on MPI. The current release runs under Linux and Windows, and will Xprobably work on other varieties of Unix as well. X XWWW: http://mpiblast.lanl.gov/ END-of-mpiblast/pkg-descr echo x - mpiblast/pkg-message sed 's/^X//' >mpiblast/pkg-message << 'END-of-mpiblast/pkg-message' X-------------------------------------------------------------------------- X XThe mpiBLAST package has been successfully installed. X XNB: A sample configuration file has been installed to %%PREFIX%%/etc as X"mpiblast.conf.sample". This may be renamed to "mpiblast.conf" and edited Xto suit the requirements of a particular site. X XPlease read %%DOCSDIR%%/README file for detail. X X-------------------------------------------------------------------------- END-of-mpiblast/pkg-message echo x - mpiblast/pkg-plist sed 's/^X//' >mpiblast/pkg-plist << 'END-of-mpiblast/pkg-plist' Xbin/mpiblast Xbin/mpiformatdb Xetc/mpiblast.conf Xetc/mpiblast.conf.sample X%%PORTDOCS%%%%DOCSDIR%%/AUTHORS X%%PORTDOCS%%%%DOCSDIR%%/COPYING X%%PORTDOCS%%%%DOCSDIR%%/ChangeLog X%%PORTDOCS%%%%DOCSDIR%%/INSTALL X%%PORTDOCS%%%%DOCSDIR%%/LICENSE X%%PORTDOCS%%%%DOCSDIR%%/NEWS X%%PORTDOCS%%%%DOCSDIR%%/README X%%PORTDOCS%%%%DOCSDIR%%/TODO X%%DATADIR%%/WWWBlastWrap.pl X@dirrm %%DATADIR%% X@dirrm %%DOCSDIR%% END-of-mpiblast/pkg-plist echo c - mpiblast/files mkdir -p mpiblast/files > /dev/null 2>&1 echo x - mpiblast/files/patch-src_Makefile.in sed 's/^X//' >mpiblast/files/patch-src_Makefile.in << 'END-of-mpiblast/files/patch-src_Makefile.in' X X$FreeBSD$ X X--- src/Makefile.in.orig X+++ src/Makefile.in X@@ -184,7 +184,7 @@ X mpiblast_SOURCES = $(mpiblastsrc) X EXTRA_mpiblast_SOURCES = getopt.c getopt.h getopt1.c X X-mpiblast_LDADD = @GETOPT_LONG_SYSTEM@ @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lpthread X+mpiblast_LDADD = @GETOPT_LONG_SYSTEM@ @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lc_r X mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ X mpiblast_CPPFLAGS = -DUSING_MPI X X@@ -194,7 +194,7 @@ X X mpiformatdb_SOURCES = $(mpiformatdbsrc) X X-mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lpthread X+mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lc_r X mpiformatdb_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ formatdb X X mpiformatdb_INCLUDES = -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ END-of-mpiblast/files/patch-src_Makefile.in echo x - mpiblast/files/patch-src_Makefile.am sed 's/^X//' >mpiblast/files/patch-src_Makefile.am << 'END-of-mpiblast/files/patch-src_Makefile.am' X X$FreeBSD$ X X--- src/Makefile.am.orig X+++ src/Makefile.am X@@ -69,7 +69,7 @@ X mpiblast_SOURCES = $(mpiblastsrc) X EXTRA_mpiblast_SOURCES = getopt.c getopt.h getopt1.c X X-mpiblast_LDADD = @GETOPT_LONG_SYSTEM@ @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lpthread X+mpiblast_LDADD = @GETOPT_LONG_SYSTEM@ @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lc_r X mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ X mpiblast_CPPFLAGS = -DUSING_MPI X X@@ -78,7 +78,7 @@ X fragment_list.cpp fragment_list.hpp db_spec.hpp db_spec.cpp X mpiformatdb_SOURCES = $(mpiformatdbsrc) X X-mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lpthread X+mpiformatdb_LDADD = @GETOPT_LONG_SYSTEM@ formatdb.o @CONFIG_NCBIDIR@/build/ncbithr.o -lncbitool -lncbiobj -lncbi -L@CONFIG_NCBIDIR@/lib/ -lm -lc_r X mpiformatdb_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ formatdb X X mpiformatdb_INCLUDES = -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ END-of-mpiblast/files/patch-src_Makefile.am exit ----------------------------