Date: Mon, 24 Sep 2012 13:20:36 GMT From: Jason Bacon <jwbacon@tds.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/171918: New port: biology/plink Message-ID: <201209241320.q8ODKaAt003384@red.freebsd.org> Resent-Message-ID: <201209241330.q8ODU943020911@freefall.freebsd.org>
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>Number: 171918 >Category: ports >Synopsis: New port: biology/plink >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 Sep 24 13:30:09 UTC 2012 >Closed-Date: >Last-Modified: >Originator: Jason Bacon >Release: 9.0-RELEASE >Organization: Acadix Consulting, LLC >Environment: FreeBSD sculpin.jbacon.dyndns.org 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan 3 07:46:30 UTC 2012 root@farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC amd64 >Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. >How-To-Repeat: >Fix: Patch attached with submission follows: # 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: # # plink # plink/pkg-descr # plink/Makefile # plink/distinfo # plink/files # plink/files/patch-Makefile # echo c - plink mkdir -p plink > /dev/null 2>&1 echo x - plink/pkg-descr sed 's/^X//' >plink/pkg-descr << '13db0b698fc1987e35a2140396ca451a' XPLINK is a free, open-source whole genome association analysis toolset, Xdesigned to perform a range of basic, large-scale analyses in a Xcomputationally efficient manner. X XWWW: http://pngu.mgh.harvard.edu/~purcell/plink/ 13db0b698fc1987e35a2140396ca451a echo x - plink/Makefile sed 's/^X//' >plink/Makefile << '3225f885242ffc903c9410142479cfcd' X# New ports collection makefile for: plink X# Date created: 06 September 2012 X# Whom: Jason Bacon <jwbacon@tds.net> X# X# $FreeBSD$ X# X XPORTNAME= plink XPORTVERSION= 1.07 XCATEGORIES= biology science XMASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ XDISTNAME= ${PORTNAME}-${PORTVERSION}-src X XMAINTAINER= jwbacon@tds.net XCOMMENT= Whole genome association analysis toolset X XLICENSE= GPLv2 X XLIB_DEPENDS= lapack:${PORTSDIR}/math/lapack X XUSE_ZIP= yes XUSE_GMAKE= yes XUSE_FORTRAN= yes # Make it use the same compiler as lapack X XPLIST_FILES= bin/plink X Xdo-install: X ${MKDIR} ${PREFIX}/bin X ${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin X X.include <bsd.port.mk> 3225f885242ffc903c9410142479cfcd echo x - plink/distinfo sed 's/^X//' >plink/distinfo << 'a7e532cb61dd2baca4095cee307ed431' XSHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b XSIZE (plink-1.07-src.zip) = 2257297 a7e532cb61dd2baca4095cee307ed431 echo c - plink/files mkdir -p plink/files > /dev/null 2>&1 echo x - plink/files/patch-Makefile sed 's/^X//' >plink/files/patch-Makefile << 'b45708355594ed1e96bc7248f5f1076c' X--- Makefile.orig 2009-10-10 11:00:20.000000000 -0500 X+++ Makefile 2012-09-07 08:24:26.000000000 -0500 X@@ -26,7 +26,7 @@ X WITH_WEBCHECK = 1 X FORCE_32BIT = X WITH_ZLIB = 1 X-WITH_LAPACK = X+WITH_LAPACK = 1 X FORCE_DYNAMIC = X X # Put C++ compiler here; Windows has it's own specific version X@@ -34,17 +34,17 @@ X CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe X X # Any other compiler flags here ( -Wall, -g, etc) X-CXXFLAGS = X+# CXXFLAGS = X X # Misc X-LIB_LAPACK = /usr/lib/liblapack.so.3 X+LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran X X X # -------------------------------------------------------------------- X # Do not edit below this line X # -------------------------------------------------------------------- X X-CXXFLAGS += -O3 -I. X+CXXFLAGS += -I. X OUTPUT = plink X X # Some system specific flags X@@ -58,8 +58,8 @@ X endif X X ifeq ($(SYS),UNIX) X- CXXFLAGS += -DUNIX X- CXX = $(CXX_UNIX) X+ CXXFLAGS += -DUNIX -Dfopen64=fopen X+ CXX ?= $(CXX_UNIX) X ifndef FORCE_DYNAMIC X CXXFLAGS += -static X endif X@@ -128,7 +128,7 @@ X LIB += -ldl X endif X ifeq ($(SYS),UNIX) X-LIB += -ldl -lcrypt X+LIB += -lcrypt X endif X endif X b45708355594ed1e96bc7248f5f1076c exit >Release-Note: >Audit-Trail: >Unformatted:
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