[med-svn] [Git][med-team/bedtools][master] 8 commits: tweak floating point for *i386
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Feb 4 14:19:08 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / bedtools
Commits:
f2d47f97 by Michael R. Crusoe at 2019-02-04T13:55:23Z
tweak floating point for *i386
- - - - -
8c83bb1d by Michael R. Crusoe at 2019-02-04T13:55:23Z
print compilation commands
- - - - -
9804ec1c by Michael R. Crusoe at 2019-02-04T14:07:26Z
Don't overwrite CXXFLAGS
- - - - -
677ecd6c by Michael R. Crusoe at 2019-02-04T14:14:57Z
disable shuffle test for *i386
- - - - -
f2b53eeb by Michael R. Crusoe at 2019-02-04T14:14:58Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
a6c659b7 by Michael R. Crusoe at 2019-02-04T14:14:58Z
Remove trailing whitespace in debian/changelog
- - - - -
528e2745 by Michael R. Crusoe at 2019-02-04T14:14:58Z
Remove trailing whitespace in debian/copyright
- - - - -
abedeb21 by Michael R. Crusoe at 2019-02-04T14:14:58Z
mark bedtools-test as Multi-Arch: foreign
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/flag_no_overwrite
- + debian/patches/louder
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+bedtools (2.27.1+dfsg-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Print compilation commands
+ * For *i386: use -ffloat-store; disable shuffle tests. Closes: #890116
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Remove trailing whitespace in debian/changelog
+ * Remove trailing whitespace in debian/copyright
+ * mark bedtools-test as Multi-Arch: foreign
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 04 Feb 2019 05:33:48 -0800
+
bedtools (2.27.1+dfsg-2) unstable; urgency=medium
* Team upload
@@ -46,7 +58,7 @@ bedtools (2.26.0+dfsg-4) unstable; urgency=medium
[ Charles Plessy ]
* Distribute /usr/bin/groupBy again.
- * Conflict/Replace/Provide filo (which is being removed from Debian).
+ * Conflict/Replace/Provide filo (which is being removed from Debian).
-- Charles Plessy <plessy at debian.org> Mon, 25 Sep 2017 23:09:53 +0900
=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
python,
zlib1g-dev,
samtools
-Standards-Version: 4.1.4
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/bedtools
Vcs-Git: https://salsa.debian.org/med-team/bedtools.git
Homepage: https://github.com/arq5x/bedtools2
@@ -31,6 +31,7 @@ Description: suite of utilities for comparing genomic features
Package: bedtools-test
Architecture: all
+Multi-Arch: foreign
Depends: ${misc:Depends}
Suggests: bedtools
Breaks: bedtools (<< 2.19.1-1)
=====================================
debian/copyright
=====================================
@@ -23,7 +23,7 @@ Source: https://github.com/ekg/fastahack
Files: src/utils/BamTools/*
Copyright: © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
-License: MIT
+License: MIT
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
@@ -61,7 +61,7 @@ License: LGPL-2.1+
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Comment:
- On Debian systems, you can find a copy of the GNU Lesser General Public License
+ On Debian systems, you can find a copy of the GNU Lesser General Public License
version 2.1 in ‘/usr/share/common-licenses/LGPL-2.1’.
Name: gzstream, C++ iostream classes wrapping the zlib compression library.
=====================================
debian/patches/flag_no_overwrite
=====================================
@@ -0,0 +1,71 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Don't overwrite CXXFLAGS & include missing CPPFLAGS as needed
+--- bedtools.orig/Makefile
++++ bedtools/Makefile
+@@ -18,9 +18,9 @@
+ export UTIL_DIR = src/utils
+ export CXX = g++
+ ifeq ($(DEBUG),1)
+-export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
++export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ else
+-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
++export CXXFLAGS += -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ endif
+
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+--- bedtools.orig/src/complementFile/Makefile
++++ bedtools/src/complementFile/Makefile
+@@ -42,7 +42,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/coverageFile/Makefile
++++ bedtools/src/coverageFile/Makefile
+@@ -38,7 +38,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/subtractFile/Makefile
++++ bedtools/src/subtractFile/Makefile
+@@ -40,7 +40,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/ToolBase/Makefile
++++ bedtools/src/utils/ToolBase/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- bedtools.orig/src/utils/driver/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
=====================================
debian/patches/louder
=====================================
@@ -0,0 +1,896 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Print compilation commands
+--- bedtools.orig/src/annotateBed/Makefile
++++ bedtools/src/annotateBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+
+ clean:
+--- bedtools.orig/src/bamToBed/Makefile
++++ bedtools/src/bamToBed/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/bamToFastq/Makefile
++++ bedtools/src/bamToFastq/Makefile
+@@ -24,7 +24,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/bed12ToBed6/Makefile
++++ bedtools/src/bed12ToBed6/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/bedToBam/Makefile
++++ bedtools/src/bedToBam/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/bedToIgv/Makefile
++++ bedtools/src/bedToIgv/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/bedpeToBam/Makefile
++++ bedtools/src/bedpeToBam/Makefile
+@@ -33,7 +33,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
+--- bedtools.orig/src/closestFile/Makefile
++++ bedtools/src/closestFile/Makefile
+@@ -40,7 +40,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/clusterBed/Makefile
++++ bedtools/src/clusterBed/Makefile
+@@ -25,10 +25,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/clusterMain.o $(OBJ_DIR)/clusterBed.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/complementFile/Makefile
++++ bedtools/src/complementFile/Makefile
+@@ -42,7 +42,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/coverageFile/Makefile
++++ bedtools/src/coverageFile/Makefile
+@@ -38,7 +38,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/expand/Makefile
++++ bedtools/src/expand/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/fastaFromBed/Makefile
++++ bedtools/src/fastaFromBed/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/fisher/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/flankBed/Makefile
++++ bedtools/src/flankBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/genomeCoverageBed/Makefile
++++ bedtools/src/genomeCoverageBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/getOverlap/Makefile
++++ bedtools/src/getOverlap/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+
+ clean:
+--- bedtools.orig/src/groupBy/Makefile
++++ bedtools/src/groupBy/Makefile
+@@ -43,7 +43,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/intersectFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/jaccard/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/linksBed/Makefile
++++ bedtools/src/linksBed/Makefile
+@@ -25,10 +25,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/linksMain.o $(OBJ_DIR)/linksBed.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/mapFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/maskFastaFromBed/Makefile
++++ bedtools/src/maskFastaFromBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/mergeFile/Makefile
++++ bedtools/src/mergeFile/Makefile
+@@ -40,10 +40,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/mergeHelp.o $(OBJ_DIR)/mergeFile.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/multiBamCov/Makefile
++++ bedtools/src/multiBamCov/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/multiIntersectBed/Makefile
++++ bedtools/src/multiIntersectBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/nekSandbox1/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/nucBed/Makefile
++++ bedtools/src/nucBed/Makefile
+@@ -27,10 +27,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/nucBedMain.o $(OBJ_DIR)/nucBed.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/pairToBed/Makefile
++++ bedtools/src/pairToBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/pairToPair/Makefile
++++ bedtools/src/pairToPair/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+
+ clean:
+--- bedtools.orig/src/randomBed/Makefile
++++ bedtools/src/randomBed/Makefile
+@@ -23,7 +23,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/regressTest/Makefile
++++ bedtools/src/regressTest/Makefile
+@@ -32,9 +32,9 @@
+
+ all: #$(BUILT_OBJECTS)
+ @echo "compiling RegressTest.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(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)
++ $(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ .PHONY: all
+
+--- bedtools.orig/src/reldist/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/sampleFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/shiftBed/Makefile
++++ bedtools/src/shiftBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/shuffleBed/Makefile
++++ bedtools/src/shuffleBed/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/slopBed/Makefile
++++ bedtools/src/slopBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/sortBed/Makefile
++++ bedtools/src/sortBed/Makefile
+@@ -26,10 +26,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/sortMain.o $(OBJ_DIR)/sortBed.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/spacingFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/split/Makefile
++++ bedtools/src/split/Makefile
+@@ -25,7 +25,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/subtractFile/Makefile
++++ bedtools/src/subtractFile/Makefile
+@@ -40,7 +40,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/tagBam/Makefile
++++ bedtools/src/tagBam/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/unionBedGraphs/Makefile
++++ bedtools/src/unionBedGraphs/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/BamTools-Ancillary/Makefile
++++ bedtools/src/utils/BamTools-Ancillary/Makefile
+@@ -21,10 +21,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/BamTools/Makefile
++++ bedtools/src/utils/BamTools/Makefile
+@@ -61,7 +61,7 @@
+
+ $(OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
++ $(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
+
+ .PHONY: api
+ api:
+--- bedtools.orig/src/utils/BinTree/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+@@ -37,4 +37,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/BinTree.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/BlockedIntervals/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- bedtools.orig/src/utils/Contexts/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/Fasta/Makefile
++++ bedtools/src/utils/Fasta/Makefile
+@@ -19,7 +19,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/FileRecordTools/FileReaders/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/FileRecordTools/Makefile
++++ bedtools/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) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+ @echo " * compiling FileRecordMergeMgr.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+
+
+--- bedtools.orig/src/utils/FileRecordTools/Records/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+@@ -46,4 +46,4 @@
+ $(OBJ_DIR)/BedPlusInterval.o $(OBJ_DIR)/Bed12Interval.o $(OBJ_DIR)/BamRecord.o $(OBJ_DIR)/VcfRecord.o $(OBJ_DIR)/GffRecord.o $(OBJ_DIR)/BlockMgr.o $(OBJ_DIR)/StrandQueue.o \
+ $(OBJ_DIR)/RecordKeyList.o $(OBJ_DIR)/RecordKeyVector.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/GenomeFile/Makefile
++++ bedtools/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) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+ @echo " * compiling NewGenomeFile.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ #$(EXT_OBJECTS):
+ # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+--- bedtools.orig/src/utils/KeyListOps/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+
+ $(EXT_OBJECTS):
+@@ -41,4 +41,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/KeyListOps.o $(OBJ_DIR)/KeyListOpsMethods.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/NewChromsweep/Makefile
++++ bedtools/src/utils/NewChromsweep/Makefile
+@@ -34,10 +34,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/NewChromsweep.o $(BIN_DIR)/CloseSweep.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/RecordOutputMgr/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+@@ -38,4 +38,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/RecordOutputMgr.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/ToolBase/Makefile
++++ bedtools/src/utils/ToolBase/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+@@ -39,4 +39,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/ToolBase.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/VectorOps/Makefile
++++ bedtools/src/utils/VectorOps/Makefile
+@@ -11,10 +11,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/bedFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
+@@ -29,4 +29,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/bedFilePE/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+@@ -26,4 +26,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/bedGraphFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
+--- bedtools.orig/src/utils/chromsweep/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+@@ -29,4 +29,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/driver/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/fileType/Makefile
++++ bedtools/src/utils/fileType/Makefile
+@@ -22,10 +22,10 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/fileType.o $(OBJ_DIR)/FileRecordTypeChecker.o
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/general/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/utils/sequenceUtilities/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+@@ -26,4 +26,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/tabFile/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
+@@ -28,4 +28,4 @@
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+-.PHONY: clean
+\ No newline at end of file
++.PHONY: clean
+--- bedtools.orig/src/utils/version/Makefile
++++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/windowBed/Makefile
++++ bedtools/src/windowBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ clean:
+ @echo "Cleaning up."
+--- bedtools.orig/src/windowMaker/Makefile
++++ bedtools/src/windowMaker/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,5 @@ gzstream.h.patch
fix_test_script.patch
remove_barski_binding_site.png.patch
reproducible_build.patch
+louder
+flag_no_overwrite
=====================================
debian/rules
=====================================
@@ -5,6 +5,9 @@ export DH_VERBOSE=1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/default.mk
+ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
+ export DEB_CXXFLAGS_MAINT_APPEND=-ffloat-store
+endif
%:
dh $@
@@ -34,3 +37,14 @@ override_dh_fixperms-arch:
chmod -x $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/bedtools/genomes/*.genome
find $(CURDIR)/debian -name "*.bed" -executable -exec chmod -x \{\} \;
find $(CURDIR)/debian -name "*.sh" -not -executable -exec chmod +x \{\} \;
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
+ mv test/shuffle debian/
+endif
+ dh_auto_test
+ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
+ mv debian/shuffle test/
+endif
+endif
View it on GitLab: https://salsa.debian.org/med-team/bedtools/compare/3dd94debc43a7ea79a7c1dfa7c4077c4ebbe271b...abedeb21f62161d946d5cce15970ac7aebe43f0e
--
View it on GitLab: https://salsa.debian.org/med-team/bedtools/compare/3dd94debc43a7ea79a7c1dfa7c4077c4ebbe271b...abedeb21f62161d946d5cce15970ac7aebe43f0e
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