commit: 96adca668f64cdeb561fab922e1489e8f5aa01de Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Sat Dec 9 23:15:36 2017 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Sun Dec 10 00:05:27 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=96adca66
sci-biology/bedtools: [QA] Move patch to a distfile Closes: https://bugs.gentoo.org/620612 sci-biology/bedtools/Manifest | 3 +- sci-biology/bedtools/bedtools-2.26.0.ebuild | 7 +- .../files/bedtools-2.26.0-fix-buildsystem.patch | 869 --------------------- 3 files changed, 6 insertions(+), 873 deletions(-) diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index e398b3bee6f..642fe852658 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1 +1,2 @@ -DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2 +DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 +DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild index eeedf606deb..0520143f3d9 100644 --- a/sci-biology/bedtools/bedtools-2.26.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -9,7 +9,8 @@ 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}/${P}.tar.gz"; +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz + https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"; LICENSE="GPL-2" SLOT="0" @@ -26,7 +27,7 @@ RDEPEND="sys-libs/zlib" S="${WORKDIR}/${PN}2" DOCS=( README.md RELEASE_HISTORY ) -PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) +PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) src_configure() { append-lfs-flags diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch deleted file mode 100644 index fb6be18d707..00000000000 --- a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch +++ /dev/null @@ -1,869 +0,0 @@ -* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308) -* Remove CXX and CXXFLAGS, ebuild sets them -* Handle python via Gentoo's EPYTHON instead - ---- a/Makefile -+++ b/Makefile -@@ -16,17 +16,9 @@ - export BIN_DIR = bin - export SRC_DIR = src - export UTIL_DIR = src/utils --export CXX = g++ --ifeq ($(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/
