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Code Issues Projects Releases Wiki Activity

sci-biology/bedtools: [QA] Move patch to a distfile

Browse Source 
Closes: https://bugs.gentoo.org/620612
This commit is contained in:
Michał Górny
2017-12-10 00:15:36 +01:00
parent ecf3fdfc9f
commit 96adca668f
3 changed files with 6 additions and 873 deletions
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3
sci-biology/bedtools/Manifest
View File

@@ -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

7
sci-biology/bedtools/bedtools-2.26.0.ebuild
View File

@@ -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

869
sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
View File

@@ -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/