debian/changelog

@@ -2,6 +2,10 @@ bowtie2 (2.3.5.1-3) unstable; urgency=medium
 
   * Team upload.
   * Enable all architectures via simde.
+  * Unset M64_FLAG and POPCNT_CAPABILITY on non AMD64 archs.
+  * debian/rules: Fix testing in with cowdancer or eatmydata by unsetting
+    LD_PRELOAD (the address sanitizer must be first in the library list)
+  * Added missing ${perl:Depends} for the bowtie2 binary package
 
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 14 Dec 2019 13:42:14 +0100
 

debian/control

@@ -23,7 +23,8 @@ Package: bowtie2
 Architecture: any
 Depends: python3,
          ${misc:Depends},
-         ${shlibs:Depends}
+         ${shlibs:Depends},
+         ${perl:Depends}
 Suggests: bowtie2-examples
 Description: ultrafast memory-efficient short read aligner
  is an ultrafast and memory-efficient tool for aligning sequencing reads

debian/rules

@@ -13,8 +13,11 @@ export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
 
 EXTRA_OPTIONS =
 ifneq ($(DEB_HOST_ARCH),amd64)
-        EXTRA_OPTIONS = NO_TBB=1
+        EXTRA_OPTIONS += NO_TBB=1 POPCNT_CAPABILITY= M64_FLAG=
+else
+        EXTRA_OPTIONS += POPCNT_CAPABILITY=1 M64_FLAG=-m64
 endif
+
 export EXTRA_OPTIONS
 
 %:
@@ -36,7 +39,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	  bowtie2-align-l-sanitized \
 	  bowtie2-build-s-sanitized \
 	  bowtie2-build-l-sanitized
-	make -j1 test
+	env --unset=LD_PRELOAD make -j1 test
 endif
 
 override_dh_auto_install:
@@ -47,15 +50,15 @@ override_dh_install:
 
 override_dh_installman:
 	mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
-	debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"
-	debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"
-	debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"
-	debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"
-	debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"
-	debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"
-	debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"
-	debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
-	debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
+	env --unset=LD_PRELOAD debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
 	rm -f $(CURDIR)/debian/$(pkg)/usr/bin/bowtie2-buildc
 
 override_dh_installchangelogs: