Michael R. Crusoe pushed to branch master at Debian Med / htslib
Commits: e6a24d17 by Michael R. Crusoe at 2019-01-02T15:44:53Z enable float precisionpatch and remove -O0 from ppc64el - - - - - 4e88f3d9 by Michael R. Crusoe at 2019-01-03T08:48:49Z add SSE flags for i386 to the pkg-config. - - - - - 6b8f3065 by Michael R. Crusoe at 2019-01-03T09:13:35Z test - - - - - f08c619b by Michael R. Crusoe at 2019-01-03T09:42:00Z back out the floating point patch again. - - - - - 5 changed files: - debian/changelog - + debian/i386-htslib.pc.in - debian/patches/fix_float_precision - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +htslib (1.9-9) UNRELEASED; urgency=medium + + * add SSE flags for i386 to the pkg-config. + + -- Michael R. Crusoe <[email protected]> Wed, 02 Jan 2019 06:34:33 -0800 + htslib (1.9-8) unstable; urgency=medium * Disable optimization on ppc64el to unblock this and many other packages ===================================== debian/i386-htslib.pc.in ===================================== @@ -0,0 +1,15 @@ +includedir=@-includedir@ +libdir=@-libdir@ + +# Flags and libraries needed when linking against a static libhts.a +# (used by manual and semi-manual pkg-config(1)-style enquiries). +static_ldflags=@static_LDFLAGS@ +static_libs=@static_LIBS@ + +Name: htslib +Description: C library for high-throughput sequencing data formats +Version: @-PACKAGE_VERSION@ +Cflags: -I${includedir} -msse -mfpmath=sse +Libs: -L${libdir} -lhts +Libs.private: -L${libdir} @private_LIBS@ -lhts -lm -lpthread +Requires.private: zlib @pc_requires@ ===================================== debian/patches/fix_float_precision ===================================== @@ -3,15 +3,7 @@ Subject: ppc64el float handling fix I dug a bit further and it looks like that sam_parse1() is actually generating a different value for the floats in question, so when they are -loaded back for the comparison they are already screwed up, e.g.: - --- O3 -- -0xc0490fcf --3.14158988 - --- O0 -- -0xc0490fd0 --3.14159012 (expected) +loaded back for the comparison they are already screwed up because strtod() is used in float_to_le() and so also in u32_to_le(), which are inlined and float_to_le() takes a float and not a double as the first argument ===================================== debian/patches/series ===================================== @@ -1,4 +1,4 @@ define_PATH_MAX.patch fPIC.patch testShebang.patch -#fix_float_precision # doesn't fix all errors on ppc64el yet +#fix_float_precision ===================================== debian/rules ===================================== @@ -10,12 +10,8 @@ include /usr/share/dpkg/default.mk ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386)) DEB_CFLAGS_MAINT_APPEND=-msse -mfpmath=sse endif -ifneq (,$(filter $(DEB_HOST_ARCH),ppc64el)) - DEB_CFLAGS_MAINT_APPEND+=-O0 -else - DEB_CFLAGS_MAINT_APPEND+=-flto - DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto -endif +DEB_CFLAGS_MAINT_APPEND+=-flto +DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto export DEB_CFLAGS_MAINT_APPEND export DEB_LDFLAGS_MAINT_APPEND @@ -24,6 +20,10 @@ export DEB_LDFLAGS_MAINT_APPEND dh $@ override_dh_auto_configure: +ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386)) + cp htslib.pc.in debian/ + cp debian/i386-htslib.pc.in ./htslib.pc.in +endif # create clean copy of test dir cp -a test test_backup autoconf @@ -34,18 +34,15 @@ override_dh_auto_build: CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \ -# re-try later LDLIBS=-lhts \ PACKAGE_VERSION="$(DEB_VERSION)" \ libdir=/usr/lib/$(DEB_HOST_MULTIARCH) +# re-try later LDLIBS=-lhts \ override_dh_auto_install: for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm $(CURDIR)/test/$${binary} ; \ done - dh_auto_install -- \ - prefix=/usr \ - libdir=/usr/lib/$(DEB_HOST_MULTIARCH) \ - PACKAGE_VERSION="$(DEB_VERSION)" + dh_auto_install -- prefix=/usr # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals $(RM) -r test @@ -55,5 +52,10 @@ override_dh_installchangelogs: dh_installchangelogs NEWS override_dh_auto_clean: +ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386)) +ifneq (,$(wildcard debian/htslib.pc.in)) + cp debian/htslib.pc.in ./ +endif +endif dh_auto_clean rm -rf test_backup/ View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/881c30ff24492f4b7346e6232c20526b42967c6c...f08c619b2a48f9dce44872d53973ed93e10d9d2a -- View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/881c30ff24492f4b7346e6232c20526b42967c6c...f08c619b2a48f9dce44872d53973ed93e10d9d2a You're receiving this email because of your account on salsa.debian.org.
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