[med-svn] [sambamba] 04/04: Update to upstream version 0.6.6

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sambamba.

commit f519b7df18c1dbbd1329da92a796034bc4aa1149
Author: Andreas Tille <tille at debian.org>
Date:   Sun Mar 5 13:21:29 2017 +0100

    Update to upstream version 0.6.6
---
 debian/changelog                              |  2 +-
 debian/patches/series                         |  2 +-
 debian/patches/use_debian_packaged_libs.patch | 56 ++++++++++++++++++++-------
 debian/rules                                  |  2 +-
 4 files changed, 46 insertions(+), 16 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d8f3fea..7d298b7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-sambamba (0.6.5-1) UNRELEASED; urgency=medium
+sambamba (0.6.6-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
 
diff --git a/debian/patches/series b/debian/patches/series
index 603fc00..57b0759 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-#use_debian_packaged_libs.patch
+use_debian_packaged_libs.patch
 #replace_rdmd.patch
 #guix_makefile.patch
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
index 4a2b095..af6a043 100644
--- a/debian/patches/use_debian_packaged_libs.patch
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -4,9 +4,9 @@ Desciption: Use Debian packaged lz4 and htslib
 
 --- a/Makefile
 +++ b/Makefile
-@@ -1,8 +1,7 @@
- D_COMPILER=dmd
- D_FLAGS=--compiler=dmd -IBioD -g -d#-O -release -inline # -version=serial
+@@ -2,8 +2,7 @@ D_COMPILER=dmd
+ D_FLAGS=--compiler=dmd -IBioD -IundeaD/src -g -d#-O -release -inline # -version=serial
+ LDMD=ldmd2
  
 -STATIC_LIB_PATH=-Lhtslib -Llz4/lib
 -STATIC_LIB_SUBCMD=$(STATIC_LIB_PATH) -Wl,-Bstatic -lhts -llz4 -Wl,-Bdynamic
@@ -14,17 +14,47 @@ Desciption: Use Debian packaged lz4 and htslib
  RDMD_FLAGS=--force --build-only --compiler=$(D_COMPILER) $(D_FLAGS)
  
  PLATFORM := $(shell uname -s)
-@@ -12,11 +11,11 @@ LINK_CMD=gcc -dead_strip -lphobos2-ldc -
- DMD_STATIC_LIBS=htslib/libhts.a lz4/lib/liblz4.a
- else
- LINK_CMD=gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o $(STATIC_LIB_SUBCMD) -l:libphobos2-ldc.a -l:libdruntime-ldc.a  -lrt -lpthread -lm
--DMD_STATIC_LIBS=-L-Lhtslib -L-l:libhts.a -L-l:libphobos2.a -L-Llz4/lib -L-l:liblz4.a
-+DMD_STATIC_LIBS=-L-l:lhts -L-l:libphobos2.a -L-l:llz4
+@@ -11,7 +10,7 @@ PLATFORM := $(shell uname -s)
+ ifeq "$(PLATFORM)" "Darwin"
+ 
+ LINK_CMD=gcc -dead_strip -lphobos2-ldc -ldruntime-ldc -lm -lpthread htslib/libhts.a lz4/lib/liblz4.a build/sambamba.o -o build/sambamba
+-DMD_STATIC_LIBS=htslib/libhts.a lz4/lib/liblz4.a
++DMD_STATIC_LIBS=-lhts -llz4
+ 
+ define split-debug
+ dsymutil build/sambamba -o build/sambamba.dSYM
+@@ -32,7 +31,7 @@ endef
+ 
  endif
  
+-PREREQS := ldc-version-info htslib-static lz4-static
++PREREQS := ldc-version-info
+ 
  # DMD only - this goal is used because of fast compilation speed, during development
--all: htslib-static lz4-static
-+all:
- 	mkdir -p build/
- 	rdmd --force --build-only $(D_FLAGS) $(DMD_STATIC_LIBS) -ofbuild/sambamba main.d
+ all: $(PREREQS)
+--- a/Makefile.guix
++++ b/Makefile.guix
+@@ -10,13 +10,12 @@
+ 
+ # The following two are modified by the Guix package:
+ D_COMPILER=ldc2
+-LDC_LIB_PATH=$(HOME)/.guix-profile/lib
+ 
+ DFLAGS = -wi -I. -IBioD -IundeaD/src
+ DLIBS  = $(LDC_LIB_PATH)/libphobos2-ldc.a $(LDC_LIB_PATH)/libdruntime-ldc.a
+ DLIBS_DEBUG = $(LDC_LIB_PATH)/libphobos2-ldc-debug.a $(LDC_LIB_PATH)/libdruntime-ldc-debug.a
+ RPATH  = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $(LDC_LIB_PATH)/liblz4.so))
+-LIBS   = htslib/libhts.a -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
++LIBS   = -lhts -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
+ SRC    = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard undeaD/src/undead/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
+ OBJ    = $(SRC:.d=.o) utils/ldc_version_info_.o
+ OUT    = build/sambamba
+@@ -76,7 +75,7 @@ install:
+ 	install -m 0755 build/sambamba $(prefix)/bin
+ 
+ clean: clean-d
+-	cd htslib ; make clean
++	#cd htslib ; make clean
  
+ clean-d:
+ 	rm -rf build/*
diff --git a/debian/rules b/debian/rules
index e6afc4f..ef8a267 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,7 +10,7 @@ export LC_ALL=C.UTF-8
 	dh $@
 
 override_dh_auto_clean:
-	rm -rf build/
+	dh_auto_clean --buildsystem=makefile -- -f Makefile.guix
 
 override_dh_auto_build:
 	dh_auto_build --buildsystem=makefile -- -f Makefile.guix

-- 
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