Andreas Tille pushed to branch master at Debian Med / blasr
Commits:
2a0bf5c9 by Andreas Tille at 2019-01-28T10:16:25Z
Build-Depends: libblasr-dev
- - - - -
eeac917a by Andreas Tille at 2019-01-28T10:16:38Z
debhelper 12
- - - - -
77434dde by Andreas Tille at 2019-01-28T10:16:41Z
Standards-Version: 4.3.0
- - - - -
f3435072 by Andreas Tille at 2019-01-28T10:20:28Z
Cleanup d/rules
- - - - -
d52ec34b by Andreas Tille at 2019-01-28T10:21:13Z
Cleanup d/changelog
- - - - -
62aa5ad5 by Andreas Tille at 2019-01-28T12:12:44Z
Hack around diff in directory naming
- - - - -
5b874d3a by Andreas Tille at 2019-01-28T12:13:27Z
Versioned Build-Depends
- - - - -
a93e79be by Andreas Tille at 2019-01-28T12:39:02Z
Add -L$(HDF5_LIB)
- - - - -
1a096000 by Andreas Tille at 2019-01-28T13:54:17Z
Fix build
- - - - -
5759442a by Andreas Tille at 2019-01-28T14:03:32Z
Fix target dir
- - - - -
8ad394ff by Andreas Tille at 2019-01-28T14:53:30Z
Fix build
- - - - -
7 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/docs
- debian/install
- debian/patches/use_debian_packaged_pblibs.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,16 +1,18 @@
blasr (5.3.2-1) UNRELEASED; urgency=medium
+ * Team upload
+
[ Andreas Tille ]
* New upstream version
* Build-Depends: libpbdata-dev
Closes: #906811
* d/watch: point to Github since upstream is now tagging releases
* Point Vcs fields to salsa.debian.org
- * Standards-Version: 4.2.0
+ * debhelper 12
+ * Standards-Version: 4.3.0
* Build system switched from cmake to meson
- TODO:
- meson.build:57:0: ERROR: Native dependency 'libblasr' not found
- --> https://salsa.debian.org/med-team/libblasr
+ * Versioned Build-Depends: libblasr-dev
+ * Cleanup d/rules
[ Jelmer Vernooij ]
* Use secure copyright file specification URI.
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team
<[email protected].
Uploaders: Afif Elghraoui <[email protected]>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
python,
meson,
pkg-config,
@@ -13,8 +13,9 @@ Build-Depends: debhelper (>= 11~),
libpbseq-dev (>= 0~20160912),
libpbbam-dev (>= 0.18.0~),
libpbdata-dev,
- libgtest-dev
-Standards-Version: 4.2.0
+ libgtest-dev,
+ libblasr-dev (>= 5.3.1+dfsg-2)
+Standards-Version: 4.3.0
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/docs
=====================================
@@ -1,2 +1 @@
-README.md
-README.MANUAL.md
+README*
=====================================
debian/install
=====================================
@@ -1,11 +1,11 @@
-blasr usr/bin
-utils/loadPulses usr/bin
-utils/pls2fasta usr/bin
-utils/samtoh5 usr/bin
-utils/samtom4 usr/bin
-utils/samFilter usr/bin
-utils/toAfg usr/bin
-utils/sawriter usr/bin
-utils/sdpMatcher usr/bin
-utils/bax2bam/bin/* usr/bin
-utils/bam2bax/bin/* usr/bin
+# Does not belong to default build any more
+#utils/loadPulses usr/bin
+#utils/pls2fasta usr/bin
+#utils/samtoh5 usr/bin
+#utils/samtom4 usr/bin
+#utils/samFilter usr/bin
+#utils/toAfg usr/bin
+#utils/sawriter usr/bin
+#utils/sdpMatcher usr/bin
+#utils/bax2bam/bin/* usr/bin
+#utils/bam2bax/bin/* usr/bin
=====================================
debian/patches/use_debian_packaged_pblibs.patch
=====================================
@@ -1,6 +1,6 @@
--- a/meson.build
+++ b/meson.build
-@@ -51,10 +51,10 @@ blasr_thread_dep = dependency('threads',
+@@ -51,15 +51,19 @@ blasr_thread_dep = dependency('threads',
blasr_boost_dep = dependency('boost', required : true)
# pbbam
@@ -13,3 +13,23 @@
# 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]
++# missing libs for linker
++samwriter_pbdata_deps = cpp.find_library('pbdata')
++blasr_pbihdf_deps = cpp.find_library('pbihdf')
++
++blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep,
blasr_libblasr_dep, blasr_zlib_dep, samwriter_pbdata_deps, blasr_pbihdf_deps]
+
+ ########################
+ # sources + executable #
+@@ -110,7 +114,8 @@ 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, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'],
++)
+
+ blasr_utils_sawriter = executable(
+ 'sawriter', files([
=====================================
debian/rules
=====================================
@@ -33,27 +33,21 @@ export DEB_CXXFLAGS_MAINT_PREPEND = $(CPPFLAGS)
-I$(PBDATA_ROOT_DIR)
dh $@ --buildsystem=meson
override_dh_auto_configure:
-# ./configure.py --shared
- LDFLAGS="-L$(HTSLIB_LIB) -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem
$(HDF5_INC)" meson -Dtests=false build .
+ LDFLAGS="-L$(HTSLIB_LIB) -L$(HDF5_LIB) -lhdf5_cpp -lhdf5"
CPPFLAGS="-isystem $(HDF5_INC)" meson -Dtests=false -Dprefix=/usr build .
-#override_dh_auto_build: main bax2bam bam2bax;
-
-.PHONY: bax2bam
bax2bam: utils/bax2bax/bin/bax2bam
utils/bax2bax/bin/bax2bam:
$(MAKE) -C utils/bax2bam
-.PHONY: bam2bax
bam2bax: utils/bam2bax/bin/bam2bax
utils/bam2bax/bin/bam2bax:
$(MAKE) -C utils/bam2bax
-# Tests require data not available in the source distribution
-override_dh_auto_test: ;
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+override_dh_auto_test:
+ echo Tests require data not available in the source distribution
+endif
-#override_dh_auto_clean: override_dh_auto_configure
-# $(MAKE) clean
-# $(MAKE) -C utils/bam2bax clean
-# $(MAKE) -C utils/bax2bam clean
-# # This is created by configure.py
-# $(RM) defines.mk
+override_dh_auto_build:
+ ln -s build obj-$(DEB_BUILD_GNU_TYPE)
+ dh_auto_build
View it on GitLab:
https://salsa.debian.org/med-team/blasr/compare/e8a1ebe7a9b05de5df9465935dbbe4a5415a01f7...8ad394ffb70fd2e90d6e923953c0eab6fb8c9277
--
View it on GitLab:
https://salsa.debian.org/med-team/blasr/compare/e8a1ebe7a9b05de5df9465935dbbe4a5415a01f7...8ad394ffb70fd2e90d6e923953c0eab6fb8c9277
You're receiving this email because of your account on salsa.debian.org.
_______________________________________________
debian-med-commit mailing list
[email protected]
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
