[med-svn] [Git][med-team/pbseqlib][master] 9 commits: New upstream version 5.3.4+dfsg
Andreas Tille
gitlab at salsa.debian.org
Fri Nov 13 09:56:31 GMT 2020
Andreas Tille pushed to branch master at Debian Med / pbseqlib
Commits:
c95a8587 by Andreas Tille at 2020-11-13T08:56:25+01:00
New upstream version 5.3.4+dfsg
- - - - -
841c1677 by Andreas Tille at 2020-11-13T08:56:25+01:00
routine-update: New upstream version
- - - - -
2a201ef9 by Andreas Tille at 2020-11-13T08:56:29+01:00
Update upstream source from tag 'upstream/5.3.4+dfsg'
Update to upstream version '5.3.4+dfsg'
with Debian dir 9b3c605dd62dfa68f84171111b77ee5ffecccc70
- - - - -
cf5297aa by Andreas Tille at 2020-11-13T08:56:29+01:00
routine-update: debhelper-compat 13
- - - - -
b5ece951 by Andreas Tille at 2020-11-13T08:56:34+01:00
routine-update: Add salsa-ci file
- - - - -
22936023 by Andreas Tille at 2020-11-13T08:56:34+01:00
routine-update: Rules-Requires-Root: no
- - - - -
c74c37df by Andreas Tille at 2020-11-13T08:56:34+01:00
routine-update: No tab in license text
- - - - -
f8ba8218 by Andreas Tille at 2020-11-13T09:26:58+01:00
Update patches
- - - - -
13a3d18d by Andreas Tille at 2020-11-13T10:55:03+01:00
More friendly dh_missing installation
- - - - -
11 changed files:
- alignment/query/PbiFilterZmwGroupQuery.cpp
- bamboo_build.sh
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/meson.patch
- debian/rules
- + debian/salsa-ci.yml
- meson.build
- + subprojects/htslib.wrap
- + subprojects/zlib.wrap
Changes:
=====================================
alignment/query/PbiFilterZmwGroupQuery.cpp
=====================================
@@ -19,7 +19,7 @@ struct PbiFilterZmwGroupQuery::PbiFilterZmwGroupQueryPrivate
/// sequentially in bam files, such as in movie.subreads.bam.
public:
PbiFilterZmwGroupQueryPrivate(const PbiFilter& filter, const DataSet& dataset)
- : reader_(new PbiFilterCompositeBamReader<Compare::None>(filter, dataset))
+ : reader_(new PbiFilterCompositeBamReader<Compare::Zmw>(filter, dataset))
, nextRecord_(boost::none)
{
}
@@ -59,7 +59,7 @@ public:
}
public:
- std::unique_ptr<PbiFilterCompositeBamReader<Compare::None>> reader_;
+ std::unique_ptr<PbiFilterCompositeBamReader<Compare::Zmw>> reader_;
boost::optional<BamRecord> nextRecord_;
};
=====================================
bamboo_build.sh
=====================================
@@ -67,7 +67,7 @@ for i in "1.10" "1.8"; do
# TODO(dseifert)
# HDF5 doesn't have pkg-config files yet
export CPPFLAGS="${HDF5_CFLAGS}"
- export LDFLAGS="-static-libstdc++ -static-libgcc ${HDF5_LIBS}"
+ export LDFLAGS="-static-libstdc++ -static-libgcc ${HDF5_LIBS} -Wl,-rpath-link,${LD_LIBRARY_PATH}"
bash scripts/ci/build.sh
bash scripts/ci/test.sh
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+pbseqlib (5.3.4+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * No tab in license text (routine-update)
+ * More friendly dh_missing installation
+
+ -- Andreas Tille <tille at debian.org> Fri, 13 Nov 2020 08:56:25 +0100
+
pbseqlib (5.3.3+dfsg-4) unstable; urgency=medium
* Breaks+Replaces: libblasr (<< 5.3.3)
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: libs
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
meson,
pkg-config,
cmake,
@@ -20,6 +20,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/pbseqlib
Vcs-Git: https://salsa.debian.org/med-team/pbseqlib.git
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
+Rules-Requires-Root: no
Package: libpbseq
Architecture: all
=====================================
debian/copyright
=====================================
@@ -22,7 +22,7 @@ License: Larsson
Files: pbdata/MD5Utils.cpp
pbdata/MD5Utils.hpp
Copyright: 1991-1992 RSA Data Security, Inc.
- 1995 Mordechai T. Abzug
+ 1995 Mordechai T. Abzug
License: RSA
Files: debian/*
=====================================
debian/patches/meson.patch
=====================================
@@ -15,16 +15,22 @@ Description: There is no point to check for gtest since its installed via Build-
'libblasr_unittest', [
--- a/meson.build
+++ b/meson.build
-@@ -57,7 +57,11 @@ libblasr_zlib_dep = dependency('zlib', r
+@@ -60,12 +60,17 @@ libblasr_htslib_dep = dependency('htslib
# clock_gettime on old glibc systems
libblasr_rt_dep = cpp.find_library('rt', required : false)
--libblasr_deps = [libblasr_boost_dep, libblasr_pbbam_dep, libblasr_zlib_dep, libblasr_rt_dep]
+# Explicitely list required HDF5 components
+# hdf5_dep = dependency('hdf5', language : 'c', required: true)
+hdf5_dep = dependency('hdf5', language : 'cpp', required : false, disabler: true)
+
-+libblasr_deps = [libblasr_boost_dep, libblasr_pbbam_dep, libblasr_zlib_dep, libblasr_rt_dep, hdf5_dep]
+ libblasr_deps = [
+ libblasr_boost_dep,
+ libblasr_pbbam_dep,
+ libblasr_zlib_dep,
+ libblasr_htslib_dep,
+- libblasr_rt_dep]
++ libblasr_rt_dep,
++ hdf5_dep]
##########
# Config #
=====================================
debian/rules
=====================================
@@ -31,18 +31,15 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-$(MAKE) -k gtest
endif
-override_dh_auto_install:
- mkdir -p debian/libpbdata-dev/usr/include/pbseq
- cp -r pbdata debian/libpbdata-dev/usr/include/pbseq/
- mkdir -p debian/libpbihdf-dev/usr/include/pbseq/
- cp -r hdf debian/libpbihdf-dev/usr/include/pbseq/
- mkdir -p debian/libblasr-dev/usr/include/pbseq/
- cp -r alignment debian/libblasr-dev/usr/include/pbseq/
+override_dh_install:
+ dh_install -p libpbdata-dev usr/include/libblasr/pbdata usr/include/pbseq
+ dh_install -p libpbihdf-dev usr/include/libblasr/hdf usr/include/pbseq
+ dh_install -p libblasr-dev usr/include/libblasr/alignment usr/include/pbseq
find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$$' -delete
# defines.mk and build.mk files are symlinks and don't
# get removed by the previous command
find debian/*/usr/include/ -name "*.mk" -delete
- dh_auto_install
+ dh_install
override_dh_auto_clean:
dh_auto_clean
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
meson.build
=====================================
@@ -1,11 +1,11 @@
project(
'libblasr',
'cpp',
- version : '5.3.3',
+ version : '5.3.4',
default_options : [
'buildtype=release',
'warning_level=3',
- 'cpp_std=c++11',
+ 'cpp_std=c++14',
'b_ndebug=false'],
license : 'BSD-3',
meson_version : '>= 0.46.0')
@@ -52,12 +52,20 @@ libblasr_boost_dep = dependency('boost', required : true)
libblasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
# zlib
-libblasr_zlib_dep = dependency('zlib', required : true)
+libblasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])
+
+# htslib
+libblasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])
# clock_gettime on old glibc systems
libblasr_rt_dep = cpp.find_library('rt', required : false)
-libblasr_deps = [libblasr_boost_dep, libblasr_pbbam_dep, libblasr_zlib_dep, libblasr_rt_dep]
+libblasr_deps = [
+ libblasr_boost_dep,
+ libblasr_pbbam_dep,
+ libblasr_zlib_dep,
+ libblasr_htslib_dep,
+ libblasr_rt_dep]
##########
# Config #
=====================================
subprojects/htslib.wrap
=====================================
@@ -0,0 +1,10 @@
+[wrap-file]
+directory = htslib-1.9
+
+source_url = https://github.com/samtools/htslib/archive/1.9.zip
+source_filename = htslib-1.9.zip
+source_hash = c4d3ae84014f8a80f5011521f391e917bc3b4f6ebd78e97f238472e95849ec14
+
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.9/1/get_zip
+patch_filename = htslib-1.9-1-wrap.zip
+patch_hash = 02f4a3c64d668d4d09f8bb0f57eb33398e90e6901989f257be6a6716a15bdcdd
=====================================
subprojects/zlib.wrap
=====================================
@@ -0,0 +1,10 @@
+[wrap-file]
+directory = zlib-1.2.11
+
+source_url = http://zlib.net/fossils/zlib-1.2.11.tar.gz
+source_filename = zlib-1.2.11.tar.gz
+source_hash = c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1
+
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/zlib/1.2.11/4/get_zip
+patch_filename = zlib-1.2.11-4-wrap.zip
+patch_hash = f733976fbfc59e0bcde01aa9469a24eeb16faf0a4280b17e9eaa60a301d75657
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/compare/4ab2b717b84e32e616817bc3a283ef5fcfbdcb4a...13a3d18d753886d42c62c89f6da3018bdc2e58f8
--
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/compare/4ab2b717b84e32e616817bc3a283ef5fcfbdcb4a...13a3d18d753886d42c62c89f6da3018bdc2e58f8
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