Change log for sra-sdk package in Ubuntu

sra-sdk (3.0.3+dfsg-6ubuntu5) noble; urgency=medium

  * No-change rebuild for CVE-2024-3094

 -- William Grant <email address hidden>  Mon, 01 Apr 2024 15:51:57 +1100

Available diffs

• diff from 3.0.3+dfsg-6ubuntu4 to 3.0.3+dfsg-6ubuntu5 (348 bytes)

sra-sdk (3.0.3+dfsg-6ubuntu4) noble; urgency=medium

  * Drop build-dependency on python3-distutils, see #1065961

 -- Graham Inggs <email address hidden>  Sat, 23 Mar 2024 12:37:41 +0000

Available diffs

• diff from 3.0.3+dfsg-6ubuntu1 to 3.0.3+dfsg-6ubuntu4 (585 bytes)
• diff from 3.0.3+dfsg-6ubuntu3 to 3.0.3+dfsg-6ubuntu4 (486 bytes)

sra-sdk (3.0.3+dfsg-6ubuntu3) noble; urgency=medium

  * No-change rebuild against libhdf5-103-1t64

 -- Steve Langasek <email address hidden>  Wed, 13 Mar 2024 18:05:54 +0000

Available diffs

• diff from 3.0.3+dfsg-6ubuntu2 to 3.0.3+dfsg-6ubuntu3 (318 bytes)

sra-sdk (3.0.3+dfsg-6ubuntu2) noble; urgency=medium

  * No-change rebuild against libssl3t64

 -- Steve Langasek <email address hidden>  Mon, 04 Mar 2024 21:25:51 +0000

Available diffs

• diff from 3.0.3+dfsg-6ubuntu1 to 3.0.3+dfsg-6ubuntu2 (345 bytes)

sra-sdk (3.0.3+dfsg-6ubuntu1) mantic; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

Available diffs

• diff from 3.0.3+dfsg-5ubuntu1 to 3.0.3+dfsg-6ubuntu1 (996 bytes)

sra-sdk (3.0.3+dfsg-5ubuntu1) mantic; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - Disable LTO; this causes a misbuild that makes fastq-dump segfault.

Available diffs

• diff from 3.0.3+dfsg-4ubuntu2 to 3.0.3+dfsg-5ubuntu1 (1.8 KiB)

sra-sdk (3.0.3+dfsg-4ubuntu2) lunar; urgency=medium

  * No-change rebuild against libre2-10

 -- Steve Langasek <email address hidden>  Sat, 04 Feb 2023 01:41:35 +0000

Available diffs

• diff from 2.11.3+dfsg-1ubuntu1 to 3.0.3+dfsg-4ubuntu2 (23.0 MiB)
• diff from 3.0.3+dfsg-4ubuntu1 to 3.0.3+dfsg-4ubuntu2 (341 bytes)

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.

Available diffs

• diff from 2.11.3+dfsg-1ubuntu1 to 3.0.3+dfsg-4ubuntu1 (23.0 MiB)

sra-sdk (2.11.3+dfsg-1ubuntu1) jammy; urgency=medium

  * Disable LTO, this causes a misbuild that makes fastq-dump segfault.

 -- Steve Langasek <email address hidden>  Tue, 05 Apr 2022 15:21:01 +0000

Available diffs

• diff from 2.10.9+dfsg-2 (in Debian) to 2.11.3+dfsg-1ubuntu1 (547.5 KiB)
• diff from 2.11.3+dfsg-1 (in Debian) to 2.11.3+dfsg-1ubuntu1 (718 bytes)

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 <email address hidden>  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 <email address hidden>  Thu, 04 Feb 2021 20:38:51 -0500

Available diffs

• diff from 2.10.7+dfsg-1 to 2.10.9+dfsg-2 (98.8 KiB)
• diff from 2.10.9+dfsg-1 to 2.10.9+dfsg-2 (1.4 KiB)

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 <email address hidden>  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 <email address hidden>  Tue, 02 Jun 2020 21:47:38 -0400

Available diffs

• diff from 2.10.6+dfsg-5 to 2.10.7+dfsg-1 (11.3 KiB)

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 <email address hidden>  Mon, 25 May 2020 22:45:07 -0400

Available diffs

• diff from 2.10.6+dfsg-4 to 2.10.6+dfsg-5 (1.1 KiB)

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 <email address hidden>  Fri, 22 May 2020 09:25:13 -0400

Available diffs

• diff from 2.10.6+dfsg-3 to 2.10.6+dfsg-4 (1.5 KiB)

sra-sdk (2.10.6+dfsg-3) unstable; urgency=medium

  * Also exclude sra-pileup check_skiplist test per network access.

 -- Aaron M. Ucko <email address hidden>  Thu, 21 May 2020 10:17:04 -0400

Available diffs

• diff from 2.10.6+dfsg-2 to 2.10.6+dfsg-3 (665 bytes)

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 <email address hidden>  Thu, 21 May 2020 09:03:42 -0400

Available diffs

• diff from 2.10.6+dfsg-1 to 2.10.6+dfsg-2 (1.1 KiB)

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 <email address hidden>  Wed, 20 May 2020 22:15:19 -0400

sra-sdk (2.9.3+dfsg-1build2) disco; urgency=medium

  * Rebuild against new libhdf5-103.

 -- Gianfranco Costamagna <email address hidden>  Wed, 12 Dec 2018 12:11:40 +0100

Available diffs

• diff from 2.9.3+dfsg-1build1 to 2.9.3+dfsg-1build2 (331 bytes)

sra-sdk (2.9.3+dfsg-1build1) disco; urgency=medium

  * No-change rebuild against libmbedtls12

 -- Steve Langasek <email address hidden>  Mon, 12 Nov 2018 20:18:14 +0000

Available diffs

• diff from 2.9.3+dfsg-1 (in Debian) to 2.9.3+dfsg-1build1 (512 bytes)

sra-sdk (2.9.3+dfsg-1) unstable; urgency=medium

  * Team upload.

  * New upstream version.

 -- Steffen Moeller <email address hidden>  Tue, 23 Oct 2018 15:12:22 +0200

Available diffs

• diff from 2.9.1-1+dfsg-2 to 2.9.3+dfsg-1 (6.5 KiB)

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 <email address hidden>  Thu, 05 Jul 2018 19:13:15 +0300

Available diffs

• diff from 2.8.2-5+dfsg-1 to 2.9.1-1+dfsg-2 (1002.5 KiB)
• diff from 2.9.1-1+dfsg-1 to 2.9.1-1+dfsg-2 (474 bytes)

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 <email address hidden>  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 <email address hidden>  Sun, 18 Feb 2018 15:44:10 +0100

Available diffs

• diff from 2.8.2-3+dfsg-1 to 2.8.2-5+dfsg-1 (16.0 KiB)

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 <email address hidden>  Mon, 04 Dec 2017 08:29:02 +0100

Available diffs

• diff from 2.8.1-2+dfsg-2 to 2.8.2-3+dfsg-1 (45.5 KiB)

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 <email address hidden>)
    Closes: #859261

 -- Andreas Tille <email address hidden>  Sat, 01 Apr 2017 23:06:00 +0200

Available diffs

• diff from 2.8.1-2+dfsg-1ubuntu1 (in Ubuntu) to 2.8.1-2+dfsg-2 (635 bytes)

sra-sdk (2.8.1-2+dfsg-1ubuntu1) zesty; urgency=medium

  * Use DEB_BUILD_GNU_TYPE instead of DEB_HOST_MULTIARCH to fix FTBFS on i386

 -- Graham Inggs <email address hidden>  Sat, 01 Apr 2017 12:15:14 +0200

Available diffs

• diff from 2.3.5-2+dfsg-1ubuntu1 to 2.8.1-2+dfsg-1ubuntu1 (4.1 MiB)
• diff from 2.8.1-2+dfsg-1 (in Debian) to 2.8.1-2+dfsg-1ubuntu1 (1.0 KiB)

sra-sdk (2.8.1-2+dfsg-1) unstable; urgency=medium

  * New upstream bugfix release

 -- Andreas Tille <email address hidden>  Tue, 24 Jan 2017 09:05:43 +0100

Available diffs

• diff from 2.8.1+dfsg-3 to 2.8.1-2+dfsg-1 (1.4 KiB)

sra-sdk (2.8.1+dfsg-3) unstable; urgency=medium

  * Upstream suggested a different name to resolve #851219: vdb-get

 -- Andreas Tille <email address hidden>  Sat, 14 Jan 2017 14:41:57 +0100

Available diffs

• diff from 2.8.1+dfsg-2 to 2.8.1+dfsg-3 (852 bytes)

sra-sdk (2.8.1+dfsg-2) unstable; urgency=medium

  * Deal with name space conflict with kget
    Closes: #851219

 -- Andreas Tille <email address hidden>  Fri, 13 Jan 2017 09:23:03 +0100

Available diffs

• diff from 2.8.1+dfsg-1 to 2.8.1+dfsg-2 (1.3 KiB)

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 <email address hidden>  Wed, 11 Jan 2017 23:06:42 +0100

Available diffs

• diff from 2.7.0-2 to 2.8.1+dfsg-1 (369.8 KiB)

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 <email address hidden>  Fri, 25 Nov 2016 19:08:25 +0100

Available diffs

• diff from 2.7.0-1 to 2.7.0-2 (1.3 KiB)

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 <email address hidden>  Thu, 01 Sep 2016 15:41:02 +0200

sra-sdk (2.3.5-2+dfsg-1ubuntu1) vivid; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - debian/control: Limit to amd64 and i386 due to some assembly.

Available diffs

• diff from 2.3.4-2+dfsg-2ubuntu1 to 2.3.5-2+dfsg-1ubuntu1 (266.5 KiB)

sra-sdk (2.3.4-2+dfsg-2ubuntu1) utopic; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - debian/control: Limit to amd64 and i386 due to some assembly.

Available diffs

• diff from 2.1.7a-1ubuntu2 to 2.3.4-2+dfsg-2ubuntu1 (1.8 MiB)
• diff from 2.3.3-4~dfsg-1ubuntu1 to 2.3.4-2+dfsg-2ubuntu1 (179.9 KiB)

sra-sdk (2.3.3-4~dfsg-1ubuntu1) trusty; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - debian/control: Limit to amd64 and i386 due to some assembly.

Available diffs

• diff from 2.1.7a-1ubuntu2 to 2.3.3-4~dfsg-1ubuntu1 (1.8 MiB)

sra-sdk (2.1.7a-1ubuntu2) quantal; urgency=low

  * Fowl ball! Missed one package to be marked as amd64/i386 only.
 -- Ben Collins <email address hidden>   Thu, 14 Jun 2012 21:57:08 -0400

Available diffs

• diff from 2.1.7a-1ubuntu1 to 2.1.7a-1ubuntu2 (547 bytes)

sra-sdk (2.1.7a-1ubuntu1) quantal; urgency=low

  * Limit to amd64 and i386 due to some assembly.
 -- Ben Collins <email address hidden>   Thu, 14 Jun 2012 01:37:16 -0400

Available diffs

• diff from 2.1.7a-1 (in Debian) to 2.1.7a-1ubuntu1 (862 bytes)

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 <email address hidden>  Tue, 10 Jan 2012 09:06:14 +0900

sra-sdk (2.0.1-1) unstable; urgency=low

  * Initial release (Closes: #610603).
 -- Ubuntu Archive Auto-Sync <email address hidden>   Wed,  25 May 2011 22:30:59 +0000