From owner-freebsd-ports-bugs@FreeBSD.ORG Tue Oct 26 07:20:23 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 7B3AC16A4CF for ; Tue, 26 Oct 2004 07:20:23 +0000 (GMT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 532FE43D45 for ; Tue, 26 Oct 2004 07:20:23 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) i9Q7KNDc007776 for ; Tue, 26 Oct 2004 07:20:23 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.11/8.12.11/Submit) id i9Q7KNsw007775; Tue, 26 Oct 2004 07:20:23 GMT (envelope-from gnats) Date: Tue, 26 Oct 2004 07:20:23 GMT Message-Id: <200410260720.i9Q7KNsw007775@freefall.freebsd.org> To: freebsd-ports-bugs@FreeBSD.org From: "Choe, Cheng-Dae" 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 07:20:23 -0000 The following reply was made to PR ports/73149; it has been noted by GNATS. From: "Choe, Cheng-Dae" To: freebsd-gnats-submit@freebsd.org, freebsd-ports-bugs@freebsd.org Cc: Subject: Re: ports/73149: [New ports]: biology/mpiblast Date: Tue, 26 Oct 2004 16:17:40 +0900 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 ----------------------------