From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 69996138330 for ; Sat, 24 Sep 2016 22:55:58 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 7E60C21C088; Sat, 24 Sep 2016 22:55:55 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 1195E21C038 for ; Sat, 24 Sep 2016 22:55:54 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 40BDC34027D for ; Sat, 24 Sep 2016 22:55:53 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id C43C82481 for ; Sat, 24 Sep 2016 22:55:50 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1474757737.c8c95dc5616fe51e1fffe9f875556a5ff14be39e.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/bedtools/Manifest sci-biology/bedtools/bedtools-2.26.0.ebuild sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch X-VCS-Directories: sci-biology/bedtools/ sci-biology/bedtools/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: c8c95dc5616fe51e1fffe9f875556a5ff14be39e X-VCS-Branch: master Date: Sat, 24 Sep 2016 22:55:50 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 9fcccaa4-892f-4054-98f4-603680719dcf X-Archives-Hash: 4d3c4e449c5772bb5f0859c754b278f0 commit: c8c95dc5616fe51e1fffe9f875556a5ff14be39e Author: David Seifert gentoo org> AuthorDate: Sat Sep 24 22:47:39 2016 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Sep 24 22:55:37 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c8c95dc5 sci-biology/bedtools: Version bump to 2.26.0 Gentoo-bug: 594994 * EAPI=6 * Make buildsystem output verbose * Inherit 'python-any-r1', due to python script * Add dependencies for test suite * Properly set CXX and CXXFLAGS Package-Manager: portage-2.3.1 sci-biology/bedtools/Manifest | 1 + sci-biology/bedtools/bedtools-2.26.0.ebuild | 42 + .../files/bedtools-2.26.0-fix-buildsystem.patch | 869 +++++++++++++++++++++ 3 files changed, 912 insertions(+) diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 9dd006e..c5daa59 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,2 +1,3 @@ DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772 SHA512 4dfeb048a7eacb1ca70caed64087d279aa955f30cf685f938e5a02ba328d1a878a75bfe37b537fc06cf9023474e4922719f1b391943ff0143c7760e987fa4645 WHIRLPOOL d6b89fdd4dc1f7bebcda71ea7b4c76c5d5811d7b23861019e19667171572743bd8dfbd74d4e80838aa4bfa06a524bcfaf5e76cd52c49b0658929b0060ee3aaa0 DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84 +DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2 diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild new file mode 100644 index 00000000..feddd87 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) + +inherit flag-o-matic python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="test" + +DEPEND="${PYTHON_DEPS} + test? ( + sci-libs/htslib + sci-biology/samtools + )" + +S="${WORKDIR}/${PN}2" + +DOCS=( README.md RELEASE_HISTORY ) +PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) + +src_configure() { + append-lfs-flags + export prefix="${EPREFIX}/usr" + tc-export AR CXX +} + +src_install() { + default + + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch new file mode 100644 index 00000000..fb6be18 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch @@ -0,0 +1,869 @@ +* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308) +* Remove CXX and CXXFLAGS, ebuild sets them +* Handle python via Gentoo's EPYTHON instead + +--- a/Makefile ++++ b/Makefile +@@ -16,17 +16,9 @@ + export BIN_DIR = bin + export SRC_DIR = src + export UTIL_DIR = src/utils +-export CXX = g++ +-ifeq ($(DEBUG),1) +-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG +-else +-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) +-endif + export LIBS = -lz + export BT_ROOT = src/utils/BamTools/ + +-prefix ?= /usr/local +- + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ + $(SRC_DIR)/bamToFastq \ +@@ -135,13 +127,13 @@ + + all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) + @echo "- Building main bedtools binary." +- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) +- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) + @echo "done." + + @echo "- Creating executables for old CLI." +- @python scripts/makeBashScripts.py +- @chmod +x bin/* ++ $(EPYTHON) scripts/makeBashScripts.py ++ chmod +x bin/* + @echo "done." + + +--- a/src/annotateBed/Makefile ++++ b/src/annotateBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/bamToBed/Makefile ++++ b/src/bamToBed/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bamToFastq/Makefile ++++ b/src/bamToFastq/Makefile +@@ -24,7 +24,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bed12ToBed6/Makefile ++++ b/src/bed12ToBed6/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bedpeToBam/Makefile ++++ b/src/bedpeToBam/Makefile +@@ -33,7 +33,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ +--- a/src/bedToBam/Makefile ++++ b/src/bedToBam/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bedToIgv/Makefile ++++ b/src/bedToIgv/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/closestFile/Makefile ++++ b/src/closestFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/clusterBed/Makefile ++++ b/src/clusterBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/complementFile/Makefile ++++ b/src/complementFile/Makefile +@@ -42,7 +42,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/coverageFile/Makefile ++++ b/src/coverageFile/Makefile +@@ -38,7 +38,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/expand/Makefile ++++ b/src/expand/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/fastaFromBed/Makefile ++++ b/src/fastaFromBed/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/fisher/Makefile ++++ b/src/fisher/Makefile +@@ -51,7 +51,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/flankBed/Makefile ++++ b/src/flankBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/genomeCoverageBed/Makefile ++++ b/src/genomeCoverageBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/getOverlap/Makefile ++++ b/src/getOverlap/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/groupBy/Makefile ++++ b/src/groupBy/Makefile +@@ -42,7 +42,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/intersectFile/Makefile ++++ b/src/intersectFile/Makefile +@@ -39,7 +39,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/jaccard/Makefile ++++ b/src/jaccard/Makefile +@@ -43,7 +43,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/linksBed/Makefile ++++ b/src/linksBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/mapFile/Makefile ++++ b/src/mapFile/Makefile +@@ -38,7 +38,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/maskFastaFromBed/Makefile ++++ b/src/maskFastaFromBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/mergeFile/Makefile ++++ b/src/mergeFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/multiBamCov/Makefile ++++ b/src/multiBamCov/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/multiIntersectBed/Makefile ++++ b/src/multiIntersectBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/nekSandbox1/Makefile ++++ b/src/nekSandbox1/Makefile +@@ -35,7 +35,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/nucBed/Makefile ++++ b/src/nucBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/pairToBed/Makefile ++++ b/src/pairToBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/pairToPair/Makefile ++++ b/src/pairToPair/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/randomBed/Makefile ++++ b/src/randomBed/Makefile +@@ -23,7 +23,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/regressTest/Makefile ++++ b/src/regressTest/Makefile +@@ -24,24 +24,18 @@ + # ---------------------------------- + # define our source and object files + # ---------------------------------- +-#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h +-#OBJECTS= regressTestMain.o RegressTest.o +-#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) ++SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h ++OBJECTS= regressTestMain.o RegressTest.o ++BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + PROGRAM= regressTest + +- +-all: #$(BUILT_OBJECTS) +- @echo "compiling RegressTest.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) +- @echo "compiling regressTestMain.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++all: $(BUILT_OBJECTS) + + .PHONY: all + +-#$(BUILT_OBJECTS): $(SOURCES) +-# @echo " * compiling" $(*F).cpp +-# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) +- ++$(BUILT_OBJECTS): $(SOURCES) ++ @echo " * compiling" $(*F).cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/reldist/Makefile ++++ b/src/reldist/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/sampleFile/Makefile ++++ b/src/sampleFile/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/shiftBed/Makefile ++++ b/src/shiftBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/shuffleBed/Makefile ++++ b/src/shuffleBed/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/slopBed/Makefile ++++ b/src/slopBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/sortBed/Makefile ++++ b/src/sortBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/spacingFile/Makefile ++++ b/src/spacingFile/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/split/Makefile ++++ b/src/split/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/subtractFile/Makefile ++++ b/src/subtractFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/tagBam/Makefile ++++ b/src/tagBam/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/unionBedGraphs/Makefile ++++ b/src/unionBedGraphs/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/BamTools/Makefile ++++ b/src/utils/BamTools/Makefile +@@ -56,12 +56,12 @@ + + $(LIBRARY): $(OBJECTS) + @echo " * linking $(LIBRARY)" +- ar cr $@ $^ ++ $(AR) cr $@ $^ + -ranlib $@ + + $(OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp + + .PHONY: api + api: +--- a/src/utils/BamTools-Ancillary/Makefile ++++ b/src/utils/BamTools-Ancillary/Makefile +@@ -21,7 +21,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/bedFile/Makefile ++++ b/src/utils/bedFile/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/bedFilePE/Makefile ++++ b/src/utils/bedFilePE/Makefile +@@ -17,7 +17,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/bedGraphFile/Makefile ++++ b/src/utils/bedGraphFile/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/BinTree/Makefile ++++ b/src/utils/BinTree/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/BlockedIntervals/Makefile ++++ b/src/utils/BlockedIntervals/Makefile +@@ -23,7 +23,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/chromsweep/Makefile ++++ b/src/utils/chromsweep/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/Contexts/Makefile ++++ b/src/utils/Contexts/Makefile +@@ -36,7 +36,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/driver/Makefile ++++ b/src/utils/driver/Makefile +@@ -85,7 +85,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/Fasta/Makefile ++++ b/src/utils/Fasta/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/FileReaders/Makefile ++++ b/src/utils/FileRecordTools/FileReaders/Makefile +@@ -32,7 +32,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/FileReaders/Makefile~ ++++ b/src/utils/FileRecordTools/FileReaders/Makefile~ +@@ -31,7 +31,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/Makefile ++++ b/src/utils/FileRecordTools/Makefile +@@ -34,9 +34,9 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling FileRecordMgr.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp + @echo " * compiling FileRecordMergeMgr.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp + + + +--- a/src/utils/FileRecordTools/Records/Makefile ++++ b/src/utils/FileRecordTools/Records/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/fileType/Makefile ++++ b/src/utils/fileType/Makefile +@@ -22,7 +22,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/general/Makefile ++++ b/src/utils/general/Makefile +@@ -21,7 +21,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/GenomeFile/Makefile ++++ b/src/utils/GenomeFile/Makefile +@@ -20,9 +20,9 @@ + + $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS) + @echo " * compiling GenomeFile.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp + @echo " * compiling NewGenomeFile.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp + + #$(EXT_OBJECTS): + # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ +--- a/src/utils/gzstream/Makefile ++++ b/src/utils/gzstream/Makefile +@@ -38,7 +38,7 @@ + UTILITIES_DIR = ../../utils/ + + ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h +- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C + + clean: + @echo "Cleaning up." +--- a/src/utils/KeyListOps/Makefile ++++ b/src/utils/KeyListOps/Makefile +@@ -31,7 +31,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + $(EXT_OBJECTS): +--- a/src/utils/NewChromsweep/Makefile ++++ b/src/utils/NewChromsweep/Makefile +@@ -34,7 +34,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/RecordOutputMgr/Makefile ++++ b/src/utils/RecordOutputMgr/Makefile +@@ -29,7 +29,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/sequenceUtilities/Makefile ++++ b/src/utils/sequenceUtilities/Makefile +@@ -17,7 +17,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/tabFile/Makefile ++++ b/src/utils/tabFile/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/ToolBase/Makefile ++++ b/src/utils/ToolBase/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/VectorOps/Makefile ++++ b/src/utils/VectorOps/Makefile +@@ -11,7 +11,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/version/Makefile ++++ b/src/utils/version/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) $(HEADERS) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/windowBed/Makefile ++++ b/src/windowBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/windowMaker/Makefile ++++ b/src/windowMaker/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/