[med-svn] [Git][med-team/htslib][master] 4 commits: enable float precisionpatch

[Michael R. Crusoe]

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 <michael.crusoe at gmail.com>  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
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