sra-sdk (3.0.3+dfsg-4ubuntu1) lunar; urgency=low
* Merge from Debian unstable. Remaining changes:
- Disable LTO; this causes a misbuild that makes fastq-dump segfault.
sra-sdk (3.0.3+dfsg-4) unstable; urgency=medium
* debian/rules: Explicitly build with signed characters (-fsigned-char).
On arm64, where char is normally unsigned, two tests otherwise fail
because messages reporting certain characters' numeric values formally
differ from expectations.
sra-sdk (3.0.3+dfsg-3) unstable; urgency=medium
* debian/copyright: Account for a second(!) version of BitMagic under
tools/loaders/bam-loader, with copyright running through 2022.
* debian/patches/no_sse4.2.patch (new): Don't use SSE 4.2. It's a
baseline violation on x86, and entirely unavailable elsewhere.
* debian/patches/use_c_locale_for_comma (new): Stick with the C locale.
en_US.UTF-8 isn't necessarily available, particularly on the buildds,
and C is perfectly sufficient to ensure recognition of comma as a
thousands separator. (Recent versions of glibc supply a middle-ground
C.utf8, but even that looks like overkill at the moment.)
sra-sdk (3.0.3+dfsg-2) unstable; urgency=medium
* Upload to unstable.
* .gitignore: Update patterns corresponding to test output.
* debian/control:
- Drop vestigial versioned dependency on libncbi-wvdb2.
- Limit architecture-dependent packages to amd64 and arm64. The only
other architecture ncbi-vdb supports is x32, but these tools require
a 64-bit address space.
* debian/not-installed: Refresh.
- Correct location of explicitly tagged lib*-static.a.
- Drop spurious entries (with hardcoded amd64 paths, no less).
* debian/patches/fix_ngs-c++-underlinkage.patch (new): Link libngs-c++
against all internal dependencies. Hold off for now on linking
against libncbi-vdb, though anyone looking to substitute libncbi-wvdb
would need to contrive to supply a suitable definition of
KDBManagerMakeRead.
* debian/patches/label_online_tests.patch: Extend as needed. All
existing labels confirmed to remain appropriate.
* debian/patches/link_vdb_dynamically.patch: Extend prior to building
tests again. To wit, additionally cover makeinputs, from
tools/loaders/general-loader/test. (All other tests were already OK at
this point.)
* debian/patches/prefer_dynamic_libraries.patch: Comment out upstream
logic that favored static linkage.
* debian/rules:
- Skip rpaths, not needed even for libhdf5.
- Explicitly enable tests, disabled by default these days.
- Update test cleanup logic to allow for build area reuse.
* debian/salsa-ci.yml: Retire remaining customizations.
sra-sdk (3.0.3+dfsg-1) experimental; urgency=medium
[ Andreas Tille ]
* Breaks+Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3)
Closes: #1024155
[ Aaron M. Ucko ]
* New upstream version.
* .gitignore:
- Unhardcode architecture name in build tree (obj-*).
- Ignore build results under ngs/ngs-python (dist, ngs.egg-info).
* debian/{control,salsa-ci.yml}: Build against libncbi-vdb-dev 3.0.1+.
* debian/copyright: Account for layout changes as of 3.0.1 and drop
references to content removed upstream, both in Files-Excluded and in
special cases.
* debian/patches: Update for 3.0.1+; in particular, account for layout
changes and better support for using system libraries.
* debian/rules:
- Correctly accommodate multiple supported Python versions. (I'd
insufficiently adapted ncbi-ngs's relevant logic.)
- Account for layout changes and CMAKE_INSTALL_LIBDIR support (with
the latter yielding multiarch paths).
- Clean up newly generated files under ngs/ngs-python.
* debian/{rules,sra-toolkit.install}: Move sratools and *-orig to a new
/usr/lib/sra-toolkit directory; repoint symlinks accordingly.
(Closes: #1025278.)
* Standards-Version: 4.6.2 (routine-update)
sra-sdk (3.0.0+dfsg-1) experimental; urgency=medium
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Build-Depends: default-jdk, flex, bison
[ Aaron M. Ucko ]
* debian/control:
- Account for consolidation of ngs-sdk (albeit with some intervening
changes, notably library restructuring); take the opportunity to add
a -java-doc package.0
- Let python3-ngs bypass libncbi-ngs-dev and use libncbi-ngs3 directly.
- Drop build dependency on libvdb-sqlite-dev, now internal to sra-sdk.
* debian/libngs-java-doc.javadoc: Enable javadoc installation.
* debian/{libngs-java.{jlibs,poms},ngs-java.pom(.asc)}: Adopt (and adapt)
from ngs-sdk.
* debian/*ngs*.examples (new): Install upstream NGS examples.
* debian/not-installed: Ignore usr/jar/*.jar (installed elsewhere, via
jh_installlibs), usr/lib64/lib*-static.a, usr/share/examples*
(installed elsewhere, via dh_installexamples), and
usr/share/javadoc/ngs-doc (installed elsewhere, via jh_installjavadoc).
* debian/patches/use_debian_packaged_re2.patch: Comment out an
inappropriate add_dependencies call in test/sharq/CMakeLists.txt.
* Add more patches for remaining build issues: fix_javadoc_build.patch,
link_magic_dynamically.patch, link_vdb_dynamically.patch, and
use_debian_packaged_compression_libs.patch.
* debian/patches/use_soversions.patch (new): Give shared libraries
proper versioned SONAMEs; use them from the Python bindings.
* debian/rules:
- Adopt (and adapt) assorted build logic from ngs-sdk.
- Pass VDB header path via -DVDB_INCDIR rather than via general
compilation flags.
- Install configuration files explicitly; the CMake setup insists on
putting them in the wrong place for us.
- Extend bin deversioning to *+ (i.e., kar+).
* debian/salsa-ci.yml: Use ncbi-vdb's aptly repo to get 3.x for now.
[ Pierre Gruet ]
* debian/control:
- Add missing build dependencies on liblzma-dev and libsam-extract-dev.
- Mark libngs-java as Architecture: all; loosen its dependencies on
libncbi-ngs-dev slightly to account for possible binNMUs.
- Introduce a libngs-jni package, on which libngs-java can and will
depend in lieu of libncbi-ngs-dev (or patching source to support
using libncbi-ngs3 directly).
* debian/libngs-java-doc.lintian-overrides: Override complaints about
javadoc-embedded jQuery per the discussion starting at
https://lists.debian.org/debian-java/2018/06/msg00020.html.
* debian/libngs-jni.links.in: Provide a general formula for libngs-jni's
central symlink.
* debian/rules: Add logic to fill in the specifics.
[ Aaron M. Ucko ]
* (debian/).gitignore (new): Ignore build and (offline) test results.
* debian/control:
- Make python3-ngs (safely!) Architecture: all too.
- Attempt Architecture: any for sra-toolkit (modulo B-D availability).
This setting matches architecture-dependent NGS packages'; if it
doesn't work out, we'll want to rein them all in for simplicity.
- Honor ${misc:Depends} for libngs-java per Lintian.
* debian/copyright: Reflect a full inventory, including convenience
copies of several third-party libraries for which it would be good to
substitute existing packages at some point.
* debian/patches/label_online_tests (new): Label tests that involve data
retrieval as "online".
* debian/patches/reflect_code_donations.patch (new): Clean up stray
licenseless copyright statements per consultation with upstream (as
quoted in the patch's header).
* debian/patches/use_stock_magic.patch (new): Let copycat use the stock
magic-number database in /usr/share/misc.
* debian/rules:
- Skip tests labeled "online" to avoid breaking on
autobuilders, which require builds to work fully offline.
- Refrain from shipping .gitignore files alongside examples.
- Clean up after tests (offline ones, anyway).
* Remove trailing whitespace in debian/changelog (routine-update)
-- Steve Langasek <email address hidden> Tue, 24 Jan 2023 21:47:16 -0800
