debian/changelog

+rapmap (0.12.0+dfsg-3) UNRELEASED; urgency=medium
+
+  * debian/patches/portable_pause: add ppc64el and arm64 alternatives to
+    asm("pause").
+  * debian/patches/no_gomp_needed: Avoid unnecessary linkage to gomp.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 01 Jan 2019 08:09:15 -0800
+
 rapmap (0.12.0+dfsg-2) unstable; urgency=medium
 
   * Add further header files to rapmap-dev since these are used in salmon

debian/control

 Source: rapmap
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille@debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+           Michael R. Crusoe <michael.crusoe@gmail.com>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11),
@@ -15,7 +16,7 @@ Build-Depends: debhelper (>= 11),
                libtclap-dev,
                pkg-config,
                python-markdown
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/rapmap
 Vcs-Git: https://salsa.debian.org/med-team/rapmap.git
 Homepage: https://github.com/COMBINE-lab/RapMap

debian/patches/no_gomp_needed

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Avoid unnecessary linkage to gomp or rt
+--- rapmap.orig/CMakeLists.txt
++++ rapmap/CMakeLists.txt
+@@ -74,7 +74,7 @@
+ set( BOOST_EXTRA_FLAGS "--layout=tagged" )
+ ## this get's set differently below if we
+ ## are on clang & apple
+-set (NON_APPLECLANG_LIBS gomp rt)
++set (NON_APPLECLANG_LIBS "$ENV{NON_APPLECLANG_LIBS}")
+ set (PTHREAD_LIB)
+ 
+ ##

debian/patches/portable_pause

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Add portable pauses
+--- rapmap.orig/include/FastxParserThreadUtils.hpp
++++ rapmap/include/FastxParserThreadUtils.hpp
+@@ -18,7 +18,13 @@
+     static const size_t MAX_BACKOFF_ITERS = 1024;
+ 
+     ALWAYS_INLINE static void cpuRelax() {
++#if defined(__aarch64__) || defined(arm64)
++      asm volatile("yield" ::: "memory");
++#elif defined(__PPC64__) || defined(PPC64) || defined(__ppc64__)
++      asm("ori 0,0,0");
++#else
+       asm("pause");
++#endif
+     }
+ 
+     ALWAYS_INLINE void yieldSleep() {

debian/patches/series

 use-debian-libs.patch
 use_shared_libs.patch
 avoid_privacy_breach.patch
+spelling
+portable_pause
+no_gomp_needed

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix typo: exeption → exception
+--- rapmap.orig/include/spdlog/details/async_log_helper.h
++++ rapmap/include/spdlog/details/async_log_helper.h
+@@ -282,7 +282,7 @@
+         }
+         catch(...)
+         {
+-            _err_handler("Unknown exeption in async logger worker loop.");
++            _err_handler("Unknown exception in async logger worker loop.");
+         }
+     }
+     if (_worker_teardown_cb) _worker_teardown_cb();

debian/rapmap.lintian-overrides

 # see https://lists.debian.org/debian-med/2018/06/msg00043.html
 rapmap: script-with-language-extension usr/bin/RunRapMap.sh
+
+# False positive
+rapmap [amd64]: spelling-error-in-binary usr/bin/rapmap YelD Yield

debian/rules

@@ -5,11 +5,18 @@
 # for hardening you might like to uncomment this:
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
+ifneq (,$(filter $(DEB_HOST_ARCH),arm64 ppc64el))
+	export NON_APPLECLANG_LIBS=z
+	# not really z, but we need something innocent here
+else
+	export NON_APPLECLANG_LIBS=rt
+endif
+
 %:
 	dh $@
 
 override_dh_auto_configure:
-	dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true
+	dh_auto_configure -- -DJELLYFISH_ROOT=/usr -DNO_NATIVE_ARCH=true $(EXTRA)
 
 override_dh_auto_build:
 	dh_auto_build