sra-sdk (3.0.3+dfsg-6~deb12u1) bookworm; urgency=medium
* Reupload to bookworm (stable).
-- Aaron M. Ucko <ucko@debian.org> Thu, 13 Jul 2023 23:08:59 -0400
sra-sdk (3.0.3+dfsg-6) unstable; urgency=high
* debian/rules: Expand $(DEB_HOST_MULTIARCH) in libngs-java.links.in.
(Closes: #1039621.)
-- Aaron M. Ucko <ucko@debian.org> Tue, 27 Jun 2023 22:14:41 -0400
sra-sdk (3.0.3+dfsg-5) unstable; urgency=medium
* Limit libngs-java to those architectures where libs are available
Closes: #1031853
* DEP3 for all patches
-- Andreas Tille <tille@debian.org> Fri, 24 Feb 2023 11:52:27 +0100
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.
-- Aaron M. Ucko <ucko@debian.org> Sun, 22 Jan 2023 17:04:21 -0500
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.)
-- Aaron M. Ucko <ucko@debian.org> Sun, 22 Jan 2023 13:26:16 -0500
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.
-- Aaron M. Ucko <ucko@debian.org> Fri, 20 Jan 2023 17:57:36 -0500
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)
-- Aaron M. Ucko <ucko@debian.org> Wed, 18 Jan 2023 21:42:39 -0500
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)
-- Aaron M. Ucko <ucko@debian.org> Sun, 13 Nov 2022 22:22:28 -0500
sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* Fix watchfile to detect new versions on github
* New upstream version 2.11.2.
* Standards-Version: 4.6.0 (routine-update)
* Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2)
* Skip test that test needs a *lot* of memory
* Link against libzstd. (Closes: #997280.)
[ Aaron M. Ucko ]
* d/p/fix_libngs_linkage.patch (new): Substitute ngs-c++ library for
absent ngs library.
* debian/rules: Stop renaming kget (to avoid a file conflict, #851219)
now that it's retired altogether.
* d/p/allow_multi_help.patch (new): Tolerate redundant --help
declarations within tools/driver-tool.
* d/p/run_unversioned_tools.patch (new): Look for tools by their
unversioned names, per Debian's simplified installation arrangement.
* debian/tests: Switch to modern encryption/decryption setup.
- run-unit-test: Replace protected repository configuration (no longer
supported as of ncbi-vdb 2.11.0) by --ngc [...].ngc.
- test-data.tar.gz: Replace dbGaP-0.enc_key by a copy of upstream's
test/prefetch/data/prj_phs710EA_test.ngc.
* debian/watch: Look for tags rather than releases, as GitHub currently
lists none(!) of the latter.
* New upstream version 2.11.3.
-- Aaron M. Ucko <ucko@debian.org> Mon, 25 Oct 2021 18:29:10 -0400
sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium
* run-unit-test: Give up for now on {abi,fastq,illumina,sff}-load.
All four rely deeply on retired VDB functionality that would be
too awkward to reintroduce.
* skip_broken_loaders.patch (new): Likewise stop building or trying to
install anything from tools/sra-load, to avoid leading users on.
-- Aaron M. Ucko <ucko@debian.org> Thu, 04 Feb 2021 20:38:51 -0500
sra-sdk (2.10.9+dfsg-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* d/watch:
- file standard 4
- Use filemangle to make sure the archive will not mixed up
with other ncbi code with same version
* Remove default debian/gbp.conf
* Bump versioned Build-Depends: libngs-sdk-dev (>= 2.10.9)
* Drop patch reenable_legacy_schema_in_sra_load.patch
-- Andreas Tille <tille@debian.org> Mon, 18 Jan 2021 09:23:28 +0100
sra-sdk (2.10.7+dfsg-1) unstable; urgency=medium
* New upstream version
* Trim trailing whitespace.
* Set field Upstream-Contact in debian/copyright.
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Remove obsolete field Contact from debian/upstream/metadata (already present
in machine-readable debian/copyright).
-- Aaron M. Ucko <ucko@debian.org> Tue, 02 Jun 2020 21:47:38 -0400
sra-sdk (2.10.6+dfsg-5) unstable; urgency=medium
* debian/patches/reenable_legacy_schema_in_sra_load.patch: New patch to
make use of ncbi-vdb's new SRAUseLegacyDefaultSchema toggle,
unbreaking tools/sra-load (fastq-load et al.) (Closes: #961347.)
* debian/control: Ensure that this toggle is available at build time and
at runtime.
-- Aaron M. Ucko <ucko@debian.org> Mon, 25 May 2020 22:45:07 -0400
sra-sdk (2.10.6+dfsg-4) unstable; urgency=medium
* Account for new sratools setup. (Closes: #961256.)
- debian/rules: Rework deversioning logic to account for sratools and
*-orig.* while still keeping hardcoding to a minimum; formally
supply a hardcoded but originally random standard installation ID in
a new /etc/ncbi/debian.kfg.
- debian/patches/use_unversioned_tools.patch (new): Have sratools look
for executable names without version extensions.
-- Aaron M. Ucko <ucko@debian.org> Fri, 22 May 2020 09:25:13 -0400
sra-sdk (2.10.6+dfsg-3) unstable; urgency=medium
* Also exclude sra-pileup check_skiplist test per network access.
-- Aaron M. Ucko <ucko@debian.org> Thu, 21 May 2020 10:17:04 -0400
sra-sdk (2.10.6+dfsg-2) unstable; urgency=medium
* drop_tests.patch: Exclude kar (needs network access); retire
test-vdb-config exclusion with (fake)root out of the picture.
Update description accordingly.
* ignore_failing_test_for_the_moment_FIXME.patch: Resync.
-- Aaron M. Ucko <ucko@debian.org> Thu, 21 May 2020 09:03:42 -0400
sra-sdk (2.10.6+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.1
* ncbi-vdb needs to appear as 2.10.2 in Debian with its mbedtls wrapper
fixed to avoid a link error in this package.
[ Michael R. Crusoe ]
* Convert to Python3. Closes: #943231
* Standards-Version: 4.5.0 (routine-update)
[ Aaron M. Ucko ]
* Correct accidental cutover to ncbi-vdb 2.10.5(+dfsg); further update to
2.10.6.
* Revert patch updates contingent on spurious cutover to ncbi-vdb.
* Refresh patches for real.
- Generally standardize on -pab format.
- hardening.patch: Rebase C(P)FLAGS, which no longer request extensions.
- python3: Drop makefile tweaks obsoleted by new PYTHON abstraction.
* Help validate-names4.c find ncbi-vdb headers that are normally internal.
To wit, build-depend on libncbi-vdb-dev (>= 2.10.6+dfsg-2~) to ensure
these headers are installed sanely, and patch validate-names4.c
accordingly in a new patch use_exposed_headers.patch. In conjunction
with taking the latest upstream, closes: #961049.
* Specify configuration location by passing KONFIG_DIR. (The makefile
patch previously in use relied on [fake]root.)
* Fix usage of default Debian build flags: Use buildflags.mk with
appropriate _APPEND settings, and tweak hardening.patch to add
DEB_*FLAGS to the front rather than the end (so as to keep upstream's
preferred optimization level).
* Preclean more fully to allow for consecutive builds.
* List (wildcard) currently uninstalled files in debian/not-installed.
* Correct logic for identifying all failing tests when there are any.
* Secure URI in copyright format (routine-update)
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Remove trailing whitespace in debian/rules (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Add myself to uploaders.
-- Aaron M. Ucko <ucko@debian.org> Wed, 20 May 2020 22:15:19 -0400
sra-sdk (2.9.4+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version.
* Bumped policy to 4.3.0
-- Steffen Moeller <moeller@debian.org> Tue, 26 Feb 2019 15:01:51 +0100
sra-sdk (2.9.3+dfsg-1) unstable; urgency=medium
* Team upload.
* New upstream version.
-- Steffen Moeller <moeller@debian.org> Tue, 23 Oct 2018 15:12:22 +0200
sra-sdk (2.9.2+dfsg-2) unstable; urgency=medium
* Architecture: amd64
-- Andreas Tille <tille@debian.org> Fri, 14 Sep 2018 08:24:15 +0200
sra-sdk (2.9.2+dfsg-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.2.1
-- Andreas Tille <tille@debian.org> Mon, 10 Sep 2018 08:25:37 +0200
sra-sdk (2.9.1-1+dfsg-2) unstable; urgency=medium
* Team upload.
* Set Build-Depends: libncbi-vdb-dev (>=2.9.1) to avoid undefined symbol
errors
-- Liubov Chuprikova <chuprikovalv@gmail.com> Thu, 05 Jul 2018 19:13:15 +0300
sra-sdk (2.9.1-1+dfsg-1) unstable; urgency=medium
* Team upload
[ Andreas Tille ]
* New upstream version
* debhelper 11
* New Build-Depends: libvdb-sqlite-dev, versioned Build-Depends
libncbi-vdb-dev (>= 2.9.0)
* Exclude strangely failing test align-cache (needs investigation)
[ Liubov Chuprikova ]
* Add autopkgtest
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Liubov Chuprikova <chuprikovalv@gmail.com> Sun, 01 Jul 2018 08:22:54 +0200
sra-sdk (2.8.2-5+dfsg-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.1.3
-- Andreas Tille <tille@debian.org> Sun, 18 Feb 2018 15:44:10 +0100
sra-sdk (2.8.2-3+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata:
- added references to registries
- yamllint cleanliness
[ Andreas Tille ]
* New upstream version
* cme fix dpkg-control
* Standards-Version: 4.1.1
* debhelper 10
* renamed function to resolve name clash with gnutards to avoid
FTBFS with glibc 2.25
Closes: #882349
* Drop test that should not run as root
-- Andreas Tille <tille@debian.org> Mon, 04 Dec 2017 08:29:02 +0100
sra-sdk (2.8.1-2+dfsg-2) unstable; urgency=medium
* Fix install dir by using DEB_HOST_MULTIARCH instead of DEB_BUILD_GNU_TYPE
(thanks for the patch to Graham Inggs <ginggs@debian.org>)
Closes: #859261
-- Andreas Tille <tille@debian.org> Sat, 01 Apr 2017 23:06:00 +0200
sra-sdk (2.8.1-2+dfsg-1) unstable; urgency=medium
* New upstream bugfix release
-- Andreas Tille <tille@debian.org> Tue, 24 Jan 2017 09:05:43 +0100
sra-sdk (2.8.1+dfsg-3) unstable; urgency=medium
* Upstream suggested a different name to resolve #851219: vdb-get
-- Andreas Tille <tille@debian.org> Sat, 14 Jan 2017 14:41:57 +0100
sra-sdk (2.8.1+dfsg-2) unstable; urgency=medium
* Deal with name space conflict with kget
Closes: #851219
-- Andreas Tille <tille@debian.org> Fri, 13 Jan 2017 09:23:03 +0100
sra-sdk (2.8.1+dfsg-1) unstable; urgency=medium
* New upstream version
Closes: #846461
* For whatever reason configure is checking for libfuse-dev so add it to
Build-Depends
* Build-Depends: libhdf5-dev, libmagic-dev, libxml2-dev
-- Andreas Tille <tille@debian.org> Wed, 11 Jan 2017 23:06:42 +0100
sra-sdk (2.7.0-2) unstable; urgency=medium
* d/rules: Remove -pie to adapt to latest changes in dpkg
* link against Debian packaged libmbedtls-dev
* Enable build using ncbi-vdb version 2.8.0
-- Andreas Tille <tille@debian.org> Fri, 25 Nov 2016 19:08:25 +0100
sra-sdk (2.7.0-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #680436, #769050
* d/watch points to github
* d/copyright: no need to exclude any files any more
* cme fix dpkg-control
* New Build-Depends: libhdf5-dev, libngs-sdk-dev (>= 1.2.4)
* drop library packages since these are now build by ncbi-vdb
* use Github as homepage
[ Steffen Moeller and Jon Ison ]
* Introduced EDAM annotation to debian/upstream/edam
-- Andreas Tille <tille@debian.org> Thu, 01 Sep 2016 15:41:02 +0200
sra-sdk (2.3.5-2+dfsg-1) unstable; urgency=medium
* New upstream version
* d/rules: Adapt get-orig-source target to new uscan implementation
* d/watch: use uversionmangle to get properly named download tarball
-- Andreas Tille <tille@debian.org> Wed, 30 Jul 2014 13:52:45 +0200
sra-sdk (2.3.4-2+dfsg-2) unstable; urgency=medium
* delete symbols file
Closes: #736411
* lintian override for no-symbols-control-file
-- Andreas Tille <tille@debian.org> Thu, 23 Jan 2014 13:41:59 +0100
sra-sdk (2.3.4-2+dfsg-1) unstable; urgency=medium
* New upstream version
* debian/control:
- Add missing Depends: sra-toolkit-libs0 to sra-toolkit-libs-dev
Closes: #715133
- Standards-Version: 3.9.5 (no changes needed)
* debian/sra-toolkit-libs0.symbols: Adapted to new upstream version
-- Andreas Tille <tille@debian.org> Mon, 23 Dec 2013 22:27:00 +0100
sra-sdk (2.3.3-4~dfsg-1) unstable; urgency=low
[ Andreas Tille ]
* New upstream version
* debian/upstream: Add citation information
* fix debian/watch
* debian/control:
- cme fix dpkg-control
- debhelper 9
- canonical Vcs fields
* debian/copyright: Exclude external libraries
* debian/rules:
- Add get-orig-source target to call enhances uscan
- remove override because upstream seems to do the correct thing now
- libsra-schema seems to be not built any more in this version so
drop the special handling of it
- Reactivate deletion of libs/krypto/*.pic.o.list files to get a
really clean source
* debian/doc: USAGE is not provided by upstream any more
* debian/patches/build-with-system-libbz2-libz.patch: Fix build problem
(thanks to Gert Wollny <gw.fossdev@gmail.com> for the patch)
* debian/sra-toolkit.install: There are neither mod?? nor wmod?? files
shipped in this version any more - so remove these from dh_install
* debian/patches/hardening.patch: Propagate Debian hardening options
into build system
* debian/patches/hardening-format-security.patch: Fix format strings in
snprintf() calls
* debian/watch: mangle version string
* debian/sra-toolkit-libs0.lintian-overrides: override
package-name-doesnt-match-sonames
[ Charles Plessy ]
32dd5cd Updated symbols file.
-- Andreas Tille <tille@debian.org> Wed, 23 Oct 2013 10:43:20 +0200
sra-sdk (2.1.7a-1) unstable; urgency=low
[ Charles Plessy ]
61e22aa New upstream release (Closes: #627861).
1b09fd5 Normalised debian/copyright file with config-edit.
a93e7b5 Wildcard characters to match 64 or 32 according to the architecture.
3d66d80 New upstream source location in debian/watch.
74e5234 Mark the use of git-buildpackage by debian/gbp.conf.
0074d68 Simplified Homepage URL in debian/control.
5cd8039 Use a target that allows dynamic linking (debian/rules).
9815817 Do not install empty /usr/bin/ncbi directory (debian/rules).
fb42792 Updated debian/sra-toolkit-libs0.symbols.
866f773 Install config.kfg and vdb-copy.kfg in /etc/ncbi.
[ Andreas Tille ]
9e6e831 Suggest patches for build system to build on non i386&amd64
architectures as well as BSD and Hurd
-- Charles Plessy <plessy@debian.org> Tue, 10 Jan 2012 09:06:14 +0900
sra-sdk (2.0.1-1) unstable; urgency=low
* Initial release (Closes: #610603).
-- Charles Plessy <plessy@debian.org> Tue, 24 May 2011 14:48:10 +0900