debian/changelog

-blasr (5.3.3+dfsg-3) UNRELEASED; urgency=medium
+blasr (5.3.3+dfsg-3) unstable; urgency=medium
 
   * Build-Depends: s/python/python3/
   * Standards-Version: 4.4.1
   * Build-Depends: cmake
   * Do not check for pbbam with meson - its ensured by Build-Depends
   * Build-Depends: libpbcopper-dev
+  * Fix meson depencencies
+    Closes: #948926
+  * rename debian/NEWS.Debian to debian/NEWS
 
- -- Andreas Tille <tille@debian.org>  Wed, 15 Jan 2020 11:16:19 +0100
+ -- Andreas Tille <tille@debian.org>  Thu, 16 Jan 2020 08:54:12 +0100
 
 blasr (5.3.3+dfsg-2) unstable; urgency=medium
 

debian/docs

 README*
-debian/NEWS*

debian/patches/use_debian_packaged_pblibs.patch

 Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 28 Jan 2019 15:56:26 +0100
+Last-Update: Thu, 16 Jan 2020 08:52:43 +0100
+Bug-Debian: https://bugs.debian.org/948926
 Description: Add some missing libraries to linker
 
 --- a/meson.build
 +++ b/meson.build
-@@ -51,15 +51,19 @@ blasr_thread_dep = dependency('threads',
+@@ -51,15 +51,21 @@ blasr_thread_dep = dependency('threads',
  blasr_boost_dep = dependency('boost', required : true)
  
  # pbbam
 -blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
-+# blasr_pbbam_dep = dependency('pbbam',  required : true)
++# blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
++blasr_pbbam_dep = cpp.find_library('pbbam')
  
  # libblasr
 -blasr_libblasr_dep = dependency('libblasr', fallback : ['blasr_libcpp', 'libblasr_dep'])
@@ -22,8 +24,45 @@ Description: Add some missing libraries to linker
 +# missing libs for linker
 +samwriter_pbdata_deps = cpp.find_library('pbdata')
 +blasr_pbihdf_deps = cpp.find_library('pbihdf')
++blasr_pbcopper_deps = cpp.find_library('pbcopper')
 +
-+blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_libblasr_dep, blasr_zlib_dep, samwriter_pbdata_deps, blasr_pbihdf_deps]
++blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_pbcopper_deps, blasr_zlib_dep, samwriter_pbdata_deps, blasr_pbihdf_deps]
  
  ########################
  # sources + executable #
+@@ -101,7 +107,7 @@ blasr_static_impl = static_library(
+   blasr_sources,
+   install : false,
+   dependencies : blasr_deps,
+-  cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1'])
++  cpp_args : [blasr_warning_flags])
+ 
+ blasr_main = executable(
+   'blasr', [
+@@ -111,7 +117,7 @@ blasr_main = executable(
+   install : true,
+   dependencies : blasr_deps,
+   link_with : blasr_static_impl,
+-  cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'])
++  cpp_args : [blasr_warning_flags, '-DCMAKE_BUILD=1'])
+ 
+ blasr_utils_sawriter = executable(
+   'sawriter', files([
+@@ -119,7 +125,7 @@ blasr_utils_sawriter = executable(
+   install : true,
+   dependencies : blasr_deps,
+   link_with : blasr_static_impl,
+-  cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'])
++  cpp_args : [blasr_warning_flags, '-DCMAKE_BUILD=1'])
+ 
+ blasr_utils_toAfg = executable(
+   'toAfg', files([
+@@ -127,7 +133,7 @@ blasr_utils_toAfg = executable(
+   install : false,
+   dependencies : blasr_deps,
+   link_with : blasr_static_impl,
+-  cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'])
++  cpp_args : [blasr_warning_flags, '-DCMAKE_BUILD=1'])
+ 
+ #########
+ # tests #

debian/rules

@@ -23,7 +23,7 @@ export LIBPBIHDF_LIB=/usr/lib/$(DEB_HOST_MULTIARCH)
 # Needed for HDF5 1.10.1 support
 HDF5_VERSION := $(shell grep 'HDF5 Version' $(HDF5_LIB)/libhdf5.settings | awk '{print $$3}')
 ifeq (yes,$(shell dpkg --compare-versions $(HDF5_VERSION) '>=' 1.10.1 && echo yes))
-export DEB_CXXFLAGS_MAINT_APPEND=-DHAVE_HDF5_1_10_1
+export DEB_CXXFLAGS_MAINT_APPEND=-DHAVE_HDF5_1_10_1 -std=c++14
 endif
 
 # CPPFLAGS apparently aren't exported for bam2bax/bax2bam