sra-sdk 3.0.3+dfsg-4ubuntu1 source package in Ubuntu

Changelog

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