[med-svn] [Git][med-team/blasr][master] 7 commits: Fix watchfile to detect new versions on github
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 8 15:15:08 BST 2021
Andreas Tille pushed to branch master at Debian Med / blasr
Commits:
1e85b936 by Andreas Tille at 2021-10-08T16:07:28+02:00
Fix watchfile to detect new versions on github
- - - - -
c2755bbb by Andreas Tille at 2021-10-08T16:07:31+02:00
New upstream version 5.3.5+dfsg
- - - - -
c6fcc083 by Andreas Tille at 2021-10-08T16:07:31+02:00
routine-update: New upstream version
- - - - -
d3845c6c by Andreas Tille at 2021-10-08T16:07:32+02:00
Update upstream source from tag 'upstream/5.3.5+dfsg'
Update to upstream version '5.3.5+dfsg'
with Debian dir 0bb0fd8478b790d82690ceb965da21feb3dd8055
- - - - -
de6bcaf0 by Andreas Tille at 2021-10-08T16:07:32+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
7103381e by Andreas Tille at 2021-10-08T16:10:56+02:00
Refresh patches
- - - - -
6284305c by Andreas Tille at 2021-10-08T16:14:48+02:00
TODO: Fix test
- - - - -
13 changed files:
- .gitignore
- Blasr.cpp
- bamboo_build.sh
- ctest/meson.build
- debian/changelog
- debian/control
- debian/patches/use_debian_packaged_pblibs.patch
- debian/watch
- iblasr/BlasrUtilsImpl.hpp
- meson.build
- + subprojects/htslib.wrap
- + subprojects/pbcopper.wrap
- + subprojects/zlib.wrap
Changes:
=====================================
.gitignore
=====================================
@@ -14,6 +14,5 @@ build/
/utils/bax2bam/tests/src/TestData.h
# Meson WrapDB stuff
-subprojects/packagecache/
-subprojects/blasr_libcpp*
-subprojects/pbbam*
+/subprojects/*
+!/subprojects/*.wrap
=====================================
Blasr.cpp
=====================================
@@ -1459,7 +1459,7 @@ int main(int argc, char *argv[])
}
delete bamWriterPtr;
bamWriterPtr = NULL;
- } catch (std::exception e) {
+ } catch (const std::exception &e) {
std::cout << "Error, could not flush bam records to bam file." << std::endl;
std::exit(EXIT_FAILURE);
}
=====================================
bamboo_build.sh
=====================================
@@ -64,7 +64,7 @@ export ENABLED_TESTS="true"
# 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
=====================================
ctest/meson.build
=====================================
@@ -41,7 +41,7 @@ blasr_test_outdir = join_paths(blasr_test_testdir, 'out')
foreach i : blasr_fast_test_list
test(
- 'blasr *' + i[1] + '* cram test: "' + i[0] + '"',
+ 'blasr cram test - ' + i[0],
blasr_cram_script,
args : [
'--xunit-file=' + join_paths(meson.build_root(), 'blasr-cram-' + i[0] + '.xml'),
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+blasr (5.3.5+dfsg-1) UNRELEASED; urgency=medium
+
+ * Fix watchfile to detect new versions on github
+ * New upstream version
+ * Standards-Version: 4.6.0 (routine-update)
+ TODO:
+md5sum: WARNING: 1 computed checksum did NOT match
+output: OK
+alignment.sam: FAILED
+autopkgtest [14:12:49]: test run-unit-test: -----------------------]
+autopkgtest [14:12:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
+run-unit-test FAIL non-zero exit status 1
+autopkgtest [14:12:49]: @@@@@@@@@@@@@@@@@@@@ summary
+run-unit-test FAIL non-zero exit status 1
+
+ -- Andreas Tille <tille at debian.org> Fri, 08 Oct 2021 16:07:31 +0200
+
blasr (5.3.3+dfsg-7) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -12,12 +12,12 @@ Build-Depends: debhelper-compat (= 13),
libhdf5-dev,
zlib1g-dev,
libpbseq-dev,
- libpbbam-dev (>= 0.18.0~),
+ libpbbam-dev,
libpbdata-dev,
libpbcopper-dev,
libgtest-dev,
libblasr-dev (>= 5.3.4+dfsg-3~)
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/blasr
Vcs-Git: https://salsa.debian.org/med-team/blasr.git
Homepage: https://github.com/PacificBiosciences/blasr
=====================================
debian/patches/use_debian_packaged_pblibs.patch
=====================================
@@ -5,12 +5,11 @@ Description: Add some missing libraries to linker
--- a/meson.build
+++ b/meson.build
-@@ -51,15 +51,19 @@ blasr_thread_dep = dependency('threads',
- blasr_boost_dep = dependency('boost', required : true)
+@@ -51,10 +51,10 @@ blasr_thread_dep = dependency('threads',
+ blasr_boost_dep = dependency('boost', include_type : 'system', required : true)
# pbbam
-blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
-+# blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
+blasr_pbbam_dep = cpp.find_library('pbbam')
# libblasr
@@ -18,17 +17,24 @@ Description: Add some missing libraries to linker
+blasr_libblasr_dep = dependency('libblasr', required : true)
# zlib
- blasr_zlib_dep = dependency('zlib', required : true)
+ blasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])
+@@ -62,11 +62,15 @@ blasr_zlib_dep = dependency('zlib', requ
+ # htslib
+ blasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])
--blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep]
+# missing libs for linker
+blasr_pbcopper_deps = cpp.find_library('pbcopper')
+
-+blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_pbcopper_deps, blasr_zlib_dep]
+ blasr_deps = [
+ blasr_thread_dep,
+ blasr_boost_dep,
+ blasr_pbbam_dep,
+ blasr_libblasr_dep,
++ blasr_pbcopper_deps,
+ blasr_zlib_dep,
+ blasr_htslib_dep]
- ########################
- # sources + executable #
-@@ -101,7 +105,7 @@ blasr_static_impl = static_library(
+@@ -110,7 +114,7 @@ blasr_static_impl = static_library(
blasr_sources,
install : false,
dependencies : blasr_deps,
@@ -37,7 +43,7 @@ Description: Add some missing libraries to linker
blasr_main = executable(
'blasr', [
-@@ -111,7 +115,7 @@ blasr_main = executable(
+@@ -120,7 +124,7 @@ blasr_main = executable(
install : true,
dependencies : blasr_deps,
link_with : blasr_static_impl,
@@ -46,7 +52,7 @@ Description: Add some missing libraries to linker
blasr_utils_sawriter = executable(
'sawriter', files([
-@@ -119,7 +123,7 @@ blasr_utils_sawriter = executable(
+@@ -128,7 +132,7 @@ blasr_utils_sawriter = executable(
install : true,
dependencies : blasr_deps,
link_with : blasr_static_impl,
@@ -55,7 +61,7 @@ Description: Add some missing libraries to linker
blasr_utils_toAfg = executable(
'toAfg', files([
-@@ -127,7 +131,7 @@ blasr_utils_toAfg = executable(
+@@ -136,7 +140,7 @@ blasr_utils_toAfg = executable(
install : false,
dependencies : blasr_deps,
link_with : blasr_static_impl,
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
- https://github.com/PacificBiosciences/blasr/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
+ https://github.com/PacificBiosciences/blasr/releases .*/v?@ANY_VERSION@@ARCHIVE_EXT@
=====================================
iblasr/BlasrUtilsImpl.hpp
=====================================
@@ -973,7 +973,7 @@ void PrintAlignment(T_AlignmentCandidate &alignment, SMRTSequence &fullRead,
SummaryOutput::Print(alignment, outFile);
}
}
- } catch (std::ostream::failure f) {
+ } catch (const std::ostream::failure &f) {
std::cout << "ERROR writing to output file. The output drive may be full, or you "
<< std::endl;
std::cout << "may not have proper write permissions." << std::endl;
=====================================
meson.build
=====================================
@@ -1,14 +1,14 @@
project(
'blasr',
'cpp',
- version : '5.3.3',
+ version : '5.3.5',
default_options : [
'buildtype=release',
'warning_level=3',
- 'cpp_std=c++11',
+ 'cpp_std=c++17',
'b_ndebug=false'],
license : 'BSD-3',
- meson_version : '>= 0.46.0')
+ meson_version : '>= 0.52.0')
# TODO:
# try to reenable 'b_ndebug=true'
@@ -48,7 +48,7 @@ endif
blasr_thread_dep = dependency('threads', required : true)
# boost
-blasr_boost_dep = dependency('boost', required : true)
+blasr_boost_dep = dependency('boost', include_type : 'system', required : true)
# pbbam
blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
@@ -57,9 +57,18 @@ blasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
blasr_libblasr_dep = dependency('libblasr', fallback : ['blasr_libcpp', 'libblasr_dep'])
# zlib
-blasr_zlib_dep = dependency('zlib', required : true)
-
-blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep]
+blasr_zlib_dep = dependency('zlib', required : true, fallback : ['zlib', 'zlib_dep'])
+
+# htslib
+blasr_htslib_dep = dependency('htslib', required : true, version : '>=1.4', fallback : ['htslib', 'htslib_dep'])
+
+blasr_deps = [
+ blasr_thread_dep,
+ blasr_boost_dep,
+ blasr_pbbam_dep,
+ blasr_libblasr_dep,
+ blasr_zlib_dep,
+ blasr_htslib_dep]
########################
# sources + executable #
=====================================
subprojects/htslib.wrap
=====================================
@@ -0,0 +1,12 @@
+[wrap-file]
+directory = htslib-1.10.2
+source_url = https://github.com/samtools/htslib/archive/1.10.2.zip
+source_filename = htslib-1.10.2.zip
+source_hash = f7994e9636f8a4032dea477a8613f5f73b330c23b5538e45666ce7306240ac14
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.10.2/1/get_zip
+patch_filename = htslib-1.10.2-1-wrap.zip
+patch_hash = 7e8a0bfef2fb17e78ba1a8fd78e152bfbcfcb941b555d88c75b6d818a07d49d1
+
+[provide]
+htslib = htslib_dep
+
=====================================
subprojects/pbcopper.wrap
=====================================
@@ -0,0 +1,4 @@
+[wrap-git]
+directory=pbcopper
+url=https://github.com/PacificBiosciences/pbcopper.git
+revision=develop
=====================================
subprojects/zlib.wrap
=====================================
@@ -0,0 +1,12 @@
+[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/1.2.11/5/get_zip
+patch_filename = zlib-1.2.11-5-wrap.zip
+patch_hash = 728c8e24acbc2e6682fbd950fec39e2fc77528af361adb87259f8a8511434004
+
+[provide]
+zlib = zlib_dep
+
View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c
--
View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/2a8fa30ecc9a3629ee55b69e32edcd3b620cc536...6284305cde9672f7df076d27a6c4c8834aad811c
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