debian/changelog

+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@gmail.com>  Mon, 04 Feb 2019 05:33:48 -0800
+
 bedtools (2.27.1+dfsg-2) unstable; urgency=medium
 
   * Team upload

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/patches/flag_no_overwrite

+From: Michael R. Crusoe <michael.crusoe@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/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