[Debian-med-packaging] Bug#878933: seqan2 FTBFS on mips64el

[Adrian Bunk]

Source: seqan2
Version: 2.3.2+dfsg2-2
Severity: serious
Tags: patch

Changes:
- don't add the CFLAGS/CPPFLAGS again when appending
  (cosmetic issue resulting in some options being set twice)
- pass -mxgot to fix link error on mips64el
  (re-using code for the no longer built mips/mipsel)
- don't overwrite CXXFLAGS with setting -DSEQAN_ASYNC_IO=0
  one of the unintended side effects was building without
  any optimization at all


--- debian/rules.old	2017-10-17 08:01:14.653184226 +0000
+++ debian/rules	2017-10-17 08:05:18.754594240 +0000
@@ -11,8 +11,8 @@
 # See https://wiki.debian.org/Hardening#Notes_for_packages_using_CMake
 DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/buildflags.mk
-CFLAGS+=$(CPPFLAGS) -O3
-CXXFLAGS+=$(CPPFLAGS) -O3
+CFLAGS+=-O3
+CXXFLAGS+=-O3
 
 # Droping -fstack-protector flag helps **drastically** reducing memory consumption when building the package!!!!
 # export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-fstack-protector *//')  ## don't do this, it simply triggers #759978
@@ -22,8 +22,8 @@
 DEB_HOST_ARCH       ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
 
 DEB_BUILD_ARCH          ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-ifneq (,$(filter mips mipsel,$(DEB_BUILD_ARCH)))
-    export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-O[1-9]//') -O1 -mxgot
+ifneq (,$(filter mips64el,$(DEB_BUILD_ARCH)))
+    export CXXFLAGS+=-mxgot
 endif
 # Disable parallel building on some build archs to save memory
 ifneq (,$(filter armhf mips kfreebsd%,$(DEB_BUILD_ARCH)))
@@ -41,7 +41,7 @@
 ifneq (,$(filter mips64el ppc64el s390x alpha hppa powerpc ppc64 sparc64,$(DEB_HOST_ARCH)))
 # Disable async io on certain target archs, as per upstream
 # https://github.com/seqan/seqan/issues/1861#issuecomment-336484553
-NOASYNC=-DCMAKE_CXX_FLAGS="-DSEQAN_ASYNC_IO=0"
+CXXFLAGS+=-DSEQAN_ASYNC_IO=0
 endif
 
 pkgapps=seqan-apps
@@ -54,7 +54,7 @@
 	#	dh_auto_configure -- -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS -DSEQAN_STATIC_APPS=False  # skip the tests for now
 	dh_auto_configure -- -DSEQAN_BUILD_SYSTEM=DEVELOP \
 		-DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \
-		-DSEQAN_DISABLE_VERSION_CHECK=YES $(NOASYNC)
+		-DSEQAN_DISABLE_VERSION_CHECK=YES
 
 override_dh_auto_configure-indep: ;