Debian
ncbi-tools6 package

Change log for ncbi-tools6 package in Debian

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Published in sid-release 
ncbi-tools6 (6.1.20170106+dfsg2-2) unstable; urgency=medium

  * Don't rely on any implicit function declarations.  (Closes: #1066356.)
    - api/asn2gnb2.c: Correct the first(!) <asn2gnbi.h> to <ffprint.h>
      for PrintDate.
    - api/salutil.c: +<alignmgr2.h> for AlnMgr2IndexSingleChildSeqAlign.
    - vibrant/shim3d.h: Add a prototype for Nlm_SetOGLContext and
      supporting forward declarations.  (Some name clashes preclude
      reliably including X headers from here.)
  * debian/control: Apply routine-update.
    - List fields in its preferred order.
    - Wrap lists to hold one item per line.
    - Standards-Version: 4.6.2 (no changes needed).
    - Drop ncbi-cn3d's Breaks/Replaces on ancient ncbi-tools-x11.

 -- Aaron M. Ucko <email address hidden>  Tue, 19 Mar 2024 23:21:24 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg2-1) unstable; urgency=medium

  * Incorporate final time64 changes; the previous two uploads used
    6.1.20170106+dfsg1-10.1~exp2 as their basis.  Adjust ...-1~exp1's
    changelog entry accordingly, dropping the Closes: annotation and the
    note about properly handling multi-library .symbols files.
  * debian/control: Trim redundant versioned build dependencies on
    dpkg-dev; a single mention in B-D should suffice.
  * debian/rules: Don't explicitly opt into time64 anywhere.  The final
    version of the NMU added a suitable versioned B-D on dpkg-dev, and the
    explicit logic (formally?) overshot on hurd-i386 and any even less
    official i386 architectures.  (RIP kfreebsd-i386.)

 -- Aaron M. Ucko <email address hidden>  Fri, 01 Mar 2024 08:59:45 -0500
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-10.1) unstable; urgency=medium

  * Non-maintainer upload.
  * Rename libraries for 64-bit time_t transition.  Closes: #1064245

 -- Steve Langasek <email address hidden>  Fri, 01 Mar 2024 10:43:06 +0000
Deleted in experimental-release (Reason: None provided.) 
ncbi-tools6 (6.1.20170106+dfsg2-1~exp2) experimental; urgency=medium

  * debian/rules: Explicitly opt back out of the time64 ABI on i386.

 -- Aaron M. Ucko <email address hidden>  Mon, 26 Feb 2024 21:38:36 -0500
Superseded in experimental-release 
ncbi-tools6 (6.1.20170106+dfsg2-1~exp1) experimental; urgency=medium

  * New tarball, with the webdesign subtree dropped; at least some of its
    content was generated but supplied without corresponding sources and
    inputs, and nothing from there was getting packaged anyway.
  * Merge initial (NMU-ed) time64 changes.  (Closes: #1064245.)
  * debian/{.gitignore,libncbi6t64.doc-base,*.lintian-overrides,*.symbols}:
    Correct stray references to old library package names.  NB: The
    initial .symbols changes missed the fact that each library package
    contained multiple libraries (not worth splitting up), and these
    lintian-overrides tuneups drop post-colon package names altogether.
  * debian/copyright (Files-Excluded):
    - Drop spurious leading ncbi/.
    - Add webdesign.
  * debian/rules: Explicitly enable the time64 ABI for now.
  * debian/watch: Update for bump to +dfsg2.

 -- Aaron M. Ucko <email address hidden>  Sun, 18 Feb 2024 21:10:49 -0500
Superseded in experimental-release 
ncbi-tools6 (6.1.20170106+dfsg1-10.1~exp2) experimental; urgency=medium

  * Non-maintainer upload.
  * Rename libraries for 64-bit time_t transition.

 -- Steve Langasek <email address hidden>  Sun, 18 Feb 2024 22:38:43 +0000
Superseded in experimental-release 
ncbi-tools6 (6.1.20170106+dfsg1-10.1~exp1) experimental; urgency=medium

  * Non-maintainer upload.
  * Rename libraries for 64-bit time_t transition.

 -- Steve Langasek <email address hidden>  Sun, 18 Feb 2024 08:25:42 +0000
Published in bookworm-release
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-10) unstable; urgency=medium

  * debian/.ncbirc: Help igblast find the auxiliary data it will ship.
  * debian/source/lintian-overrides: Ignore spurious source-is-missing for
    unwrapped text in readme.html files under network/wwwblast (but not for
    webdesign/designs/cubby/filters/ClinicalTrials.html, where it's more
    legitimate -- that file is a dump of HTML generated on an old web server).
  * Standards-Version: 4.6.1 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Reorder sequence of d/control fields by cme (routine-update)
  * Remove trailing whitespace in debian/copyright (routine-update)
  * Add salsa-ci file (routine-update)

 -- Aaron M. Ucko <email address hidden>  Fri, 02 Sep 2022 16:28:02 -0400
Published in bullseye-release
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-9) unstable; urgency=medium

  [ Andreas Tille ]
  * debian/upstream/metadata: Fix typo.

  [ Aaron M. Ucko ]
  * Trim trailing whitespace.
  * debian/copyright:
    - Use spaces rather than tabs to start continuation lines.
    - Clean up spurious trailing content on Files: lines.  (Several somehow
      wound up with trailing colons, and one had a parenthesized comment,
      which the spec doesn't allow.)
    - Correct the spelling of "downloaded."
  * Use secure URIs in Homepage field and debian/watch.
  * Bump debhelper from old 11 to 12.
  * Set debhelper-compat version in Build-Depends.
  * Move development files usable with libvibgif.so.6 to libncbi6-dev from
    libvibrant6-dev; set Breaks/Replaces accordingly.  (The runtime library
    has long been in libncbi6, since it adds no extra dependencies.)
  * debian/*.symbols: Use Build-Depends-Package, missed earlier.
  * debian/ncbi-cn3d.{postinst,prerm}: Supply -e via set, per best practice.
  * Update Lintian overrides: drop overrides associated with former .menu
    files, and go ahead and override custom-compression-in-debian-rules for
    the ncbi-rrna-data binary package, which is architecture-independent
    and benefits from tuning.
  * debian/rules: Use pkg-info.mk rather than raw dpkg-parsechangelog.

 -- Aaron M. Ucko <email address hidden>  Mon, 12 Oct 2020 22:08:56 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-8) unstable; urgency=medium

  [ Steffen Moeller ]
  * d/u/metadata: yamllint.

  [ Andreas Tille ]
  * Remove duplicate which breaks UDD import.

  [ Aaron M. Ucko ]
  * debian/control: Standards-Version: 4.5.0 (already compliant).
  * debian/ncbi-data.links (new): Establish /etc/.ncbirc (as notably
    consulted by ncbi-blast+) as a symlink to /etc/ncbi/.ncbirc (which
    this source package's binaries consult).  (LP: #1860109.)

 -- Aaron M. Ucko <email address hidden>  Sun, 16 Feb 2020 22:09:14 -0500
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-7) unstable; urgency=medium

  * debian/control: Broaden ncbi-cn3d Breaks/Replaces on ncbi-tools-x11 to
    (<= 6.1.20170106+dfsg1-5~) per delayed split.  (Closes: #940210.)

 -- Aaron M. Ucko <email address hidden>  Sat, 14 Sep 2019 20:53:39 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-6) unstable; urgency=medium

  * Reupload to unstable, having cleared NEW.

 -- Aaron M. Ucko <email address hidden>  Thu, 12 Sep 2019 21:42:48 -0400
Deleted in experimental-release (Reason: None provided.) 
ncbi-tools6 (6.1.20170106+dfsg1-5) experimental; urgency=medium

  * Split Cn3D(-3.0) out into a new ncbi-cn3d binary package; update
    debian/upstream/metadata accordingly.  (Originally done in
    6.1.20170106-7, but reverted in 6.1.20170106+dfsg1-1 to avoid holding
    up DFSG fixes.)
  * Give ncbi-cn3d a binary-specific version, missed earlier.
  * Upload to experimental to clear NEW.

 -- Aaron M. Ucko <email address hidden>  Sat, 07 Sep 2019 22:07:41 -0400
Published in stretch-release 
ncbi-tools6 (6.1.20170106+dfsg1-0+deb9u1) stretch; urgency=medium

  * Belatedly repackage without data/UniVec.*, some portions of which
    turned out to be non-free (with copyright held by Invitrogen
    Corporation, which requires a license for commercial use thereof).
  * debian/copyright:
    - Cover previously overlooked third-party code (all DFSG-free).
    - Update authors and dates for debian/*.
    - Set Files-Excluded to reflect repackaging.
  * debian/rules: Introduce NCBI_VERSION_SHLIB, with +dfsg1 stripped off.
  * debian/watch: Reflect usage of +dfsg1.
  * make/makeshlb.unx: NCBI_VERSION -> NCBI_VERSION_SHLIB.
  * Temporarily revert ncbi-cn3d splitout to expedite the above fixes.

 -- Aaron M. Ucko <email address hidden>  Sat, 03 Aug 2019 22:12:51 -0400
Published in buster-release 
ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u2) buster; urgency=medium

  * debian/ncbi-data.NEWS: Note UniVec removal, which turned out to have a
    bigger impact than anticipated.
  * debian/tests/run-unit-test: Explicitly point vecscreen at UniVec_Core.
    (See #935424.)

 -- Aaron M. Ucko <email address hidden>  Sun, 25 Aug 2019 21:15:12 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-4) unstable; urgency=medium

  * debian/NEWS: Rename from ncbi-data.NEWS to work around apt-listchanges
    bug #383803; bump version to ensure visibility.

 -- Aaron M. Ucko <email address hidden>  Mon, 26 Aug 2019 21:54:59 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-3) unstable; urgency=medium

  * debian/ncbi-data.NEWS: Note UniVec removal, which turned out to have a
    bigger impact than anticipated.
  * debian/tests/run-unit-test: Explicitly point vecscreen at UniVec_Core.
    (Closes: #935424.)

 -- Aaron M. Ucko <email address hidden>  Sun, 25 Aug 2019 21:03:24 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-2) unstable; urgency=medium

  * debian/test/run-unit-test: Substitute UniVec_Core for UniVec (removed
    in -1 per license considerations).

 -- Aaron M. Ucko <email address hidden>  Sun, 11 Aug 2019 21:59:19 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20170106+dfsg1-1) unstable; urgency=medium

  [Andreas Tille]
  * debian/upstream/metadata: Fix DOI syntax (shouldn't be a full URL).

  [Aaron M. Ucko]
  * Belatedly repackage without data/UniVec.*, some portions of which
    turned out to be non-free (with copyright held by Invitrogen
    Corporation, which requires a license for commercial use thereof.)
  * debian/copyright:
    - Cover previously overlooked third-party code (all DFSG-free).
    - Update authors and dates for debian/*.
    - Set Files-Excluded to reflect repackaging.
  * debian/rules: Introduce NCBI_VERSION_SHLIB, with +dfsg1 stripped off.
  * debian/watch: Reflect usage of +dfsg1.
  * make/makeshlb.unx: NCBI_VERSION -> NCBI_VERSION_SHLIB.
  * Temporarily revert ncbi-cn3d splitout to expedite the above fixes.

 -- Aaron M. Ucko <email address hidden>  Mon, 29 Jul 2019 22:12:41 -0400
Superseded in buster-release
Superseded in sid-release 
ncbi-tools6 (6.1.20170106-6) unstable; urgency=medium

  * debian/rules: Find indirectly needed libraries via -rpath-link rather
    than LD_LIBRARY_PATH; the -rpath-link approach is generally saner, and
    in particular has a decent shot at fully fixing cross-building.

 -- Aaron M. Ucko <email address hidden>  Thu, 27 Dec 2018 22:39:09 -0500
Superseded in sid-release 
ncbi-tools6 (6.1.20170106-5) unstable; urgency=medium

  [ Andreas Tille ]
  * Improve cross building: Don't force the build architecture compiler
    (Thanks for the patch to Helmut Grohne)
    Closes: #908353
  * cme fix dpkg-control

  [ Aaron M. Ucko ]
  * debian/control: libvibrant6b Recommends: sensible-utils (no longer
    guaranteed present, per #871260).
  * Standards-Version: 4.3.0 (already compliant).

 -- Aaron M. Ucko <email address hidden>  Mon, 24 Dec 2018 23:40:58 -0500
Superseded in buster-release
Superseded in sid-release 
ncbi-tools6 (6.1.20170106-4) unstable; urgency=medium

  * debian/compat: Advance to Debhelper 11.
  * debian/control:
    - Mark *-data reshuffling with Breaks, not just Replaces. (Closes: #902364.)
    - Build-Depends: Advance to debhelper (>= 11~).
  * debian/copyright: Fix years (packaging through 2018, upstream through 2017).

 -- Aaron M. Ucko <email address hidden>  Mon, 25 Jun 2018 21:36:10 -0400

Available diffs

Superseded in sid-release 
ncbi-tools6 (6.1.20170106-3) unstable; urgency=medium

  [ Liubov Chuprikova ]
  * Added autopkgtest for ncbi-tools-bin. 
    Closes: #879619

  [ Aaron M. Ucko ]
  * debian/{*.gif,ncbi2.css}: Add local copies of NCBI resources used by HTML
    docs.
  * debian/control:
    - Repoint Vcs-* at salsa.debian.org.
    - Standards-Version: 4.1.4 (already compliant).
    - Rules-Requires-Root: no (confirmed safe).
  * debian/{libncbi6,ncbi-tools-x11}.docs: Install resources from debian/ as
    needed.
  * debian/source/format: Set to 3.0 (quilt) to accommodate binary test data.
  * debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz
    and (individually) debian/*.gif.
  * debian/source/options: single-debian-patch (tracking changes purely
    with git for now).
  * debian/source/patch-header: "Combined patches from git."
  * demo/{findspl,taxblast_main}.c: Call SOCK_SetupSSL (accidentally missed
    earlier).
  * doc/{dispatcher,firewall}.html: Patch to use (newly supplied) local
    resources, addressing a generic privacy breach caught by Lintian.
  * make/make{demo,net}.unx: Link findspl and taxblast against $(LIBTLS)
    and $(GNUTLS_LIBS).

 -- Aaron M. Ucko <email address hidden>  Sun, 24 Jun 2018 12:06:15 -0400

Available diffs

Superseded in buster-release
Superseded in stretch-release
Superseded in sid-release 
ncbi-tools6 (6.1.20170106-2) unstable; urgency=medium

  * debian/control: Correctly version ncbi-tools-bin's Breaks/Replaces
    on blast2 over taxblast move.  (Closes: #854329.)

 -- Aaron M. Ucko <email address hidden>  Sun, 05 Feb 2017 21:40:38 -0500
Superseded in stretch-release
Superseded in sid-release 
ncbi-tools6 (6.1.20170106-1) unstable; urgency=medium

  * New upstream release (after all).
  * debian/*.symbols: Update accordingly.
  * doc/man/cleanasn.1: Update accordingly.
  * debian/copyright: Update years.

 -- Aaron M. Ucko <email address hidden>  Mon, 09 Jan 2017 22:35:15 -0500

Available diffs

Superseded in stretch-release
Superseded in sid-release 
ncbi-tools6 (6.1.20160908-2) unstable; urgency=medium

  * Stop building the transitional blast2 package (taken over by ncbi-blast+)
    and retire its remaining vestiges (the bibliograpy and autopkgtest setup).
  * connect/ncbi_util.c: Fix a FTBFS on hurd-i386 by conditionally using a
    more appropriate header for PAGE_SIZE (<mach/vm_param.h>).
  * Reinstate taxblast (now part of ncbi-tools-bin, and correctly documented
    as a postprocessing tool), accidentally dropped with the rest of blast2.

 -- Aaron M. Ucko <email address hidden>  Tue, 06 Dec 2016 18:37:19 -0500

Available diffs

Superseded in sid-release 
ncbi-tools6 (6.1.20160908-1) unstable; urgency=medium

  [ Andreas Tille ]
  * (Final) new upstream release, incorporating most Debian changes, adding
    HTTPS support, and desupporting legacy BLAST.  (Closes: #846477, #821075.)
  * cme fix dpkg-control
  * drop -dbg packages since these will be created automatically
  * Fixed watch file (thanks to Eriberto <email address hidden>)
  * DEP5

  [ Aaron M. Ucko ]
  * Reinstate direct upstream changes lost in merge.
  * Ensure that apps that could potentially hit the network can use HTTPS.
    (Don't bother with anything that only supports the old Entrez1 service.)
  * Allow Entrez2 over HTTPS by switching to the Entrez2s service, making
    HTTPS connections by default, and allowing HTTPS POST redirections from
    raw IP addresses (which NCBI's certificates don't cover).
  * Let GCC take care of setting __DATE__ and __TIME__ per SOURCE_DATE_EPOCH.
  * api/sqnutil3.c: Substitute strcpy for sprintf with no extra
    arguments, which our hardening flags disallow.
  * connect/ncbi_gnutls.c: Suppress strict version check.
  * debian/*.symbols: Update for new release.
  * debian/{blast2.*,control,rules}, make/makedemo.unx: Turn blast2 into an
    architecture-independent transitional package for ncbi-blast+-legacy.
    (Retire blastcl3, which is obsolete.)
  * debian/{compat,control}: Advance to Debhelper compat level 10.
  * debian/control: Drop unversioned B-D-I on dpkg-dev left behind by cme.
  * debian/{control,rules}:
    - Build against GNU TLS.
    - Retune ncbi-data/ncbi-rrna-data split.
  * debian/libncbi6(-dev).install, make/makeshlib.unx: Account for new
    libconnssl library.
  * debian/rules:
    - Drop override_dh_strip-arch target now that -dbg packages are gone.
    - Fix typo in name of override_dh_makeshlibs-arch target from #806084.
  * debian/{rules,.gitignore}: Stop generating legacy menu files for
    non-interactive tools (already retired in favor of XDG desktop files
    for true graphical applications). 
  * debian/rules, make/make{demo,net}.unx: Substitute -Wl,--as-needed
    for manual linkage cleanups.
  * demo/tbl2asn.c: Complain about date only if failing for other reasons.
    (Closes: #821075.)
  * doc/man/blastcl3.1: Fix a stray reference to retired programs.

 -- Aaron M. Ucko <email address hidden>  Sun, 04 Dec 2016 21:33:55 -0500
Superseded in stretch-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-12) unstable; urgency=medium

  * Team upload.
  * Autopkgtest added.

 -- Canberk Koç <email address hidden>  Sat, 20 Aug 2016 10:20:38 +0300
Superseded in stretch-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-11) unstable; urgency=medium

  * Team upload.
  * Add support for SOURCE_DATE_EPOCH, making packages building BLAST
    indexes reproducible (Closes: #834139)

 -- Sascha Steinbiss <email address hidden>  Fri, 12 Aug 2016 20:29:37 +0000
Superseded in stretch-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-10) unstable; urgency=medium

  * debian/rules: chmod +x private scripts in the targets that use them.
    (Doing so in override_dh_auto_build-arch broke indep-only builds.)

 -- Aaron M. Ucko <email address hidden>  Thu, 10 Dec 2015 01:19:59 -0500
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-9) unstable; urgency=medium

  * debian/control: Split most of Build-Depends into Build-Depends-Arch.
  * debian/makemenu: Elide menu entries, and potentially entire menu
    files, when .desktop(.in) files cover the same apps.  (See #741573.)
  * debian/rules:
    - Fix and streamline builds covering only the architecture-independent
      (*-data) packages.  (Closes: #806084.)
    - Arrange to define BUILD_{DATE,TIME} based on the last changelog entry.
    - clean: chmod -x private scripts, for compatibility with dgit.
  * debian/sbtedit.desktop.in: Add a menu entry for sbtedit, accidentally
    missed earlier.
  * {demo,sequin}/*.c: Favor BUILD_{DATE,TIME} over __DATE__ and __TIME__
    for the sake of reproducibility.
  * doc/man/sbtedit.1: Fix some minor typos.

 -- Aaron M. Ucko <email address hidden>  Wed, 09 Dec 2015 23:52:45 -0500
Superseded in stretch-release
Published in jessie-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-8) unstable; urgency=low


  [ Aaron M. Ucko ]
  * corelib/ncbimisc.c (MergeStringArray): Ensure all return paths
    explicitly return a value, as Clang reasonably requires.
  * debian/control: Formally update Standards-Version (3.9.6) and Vcs-Browser.

  [ James McCoy ]
  * Move debian/upstream to debian/upstream/metadata

 -- Aaron M. Ucko <email address hidden>  Wed, 08 Oct 2014 22:26:33 -0400

Available diffs

Superseded in jessie-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-7) unstable; urgency=low


  * debian/rules: Use find -perm /..., not deprecated +....  (Closes: #724777.)
  * debian/.gitignore: Belatedly update for switch to libvibrant6b.

 -- Aaron M. Ucko <email address hidden>  Tue, 01 Oct 2013 10:58:03 -0400

Available diffs

Superseded in jessie-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-6) unstable; urgency=low


  * debian/installman: Eliminate for $var qw(...) syntax that broke with
    Perl 5.18.  (Closes: #722913.)

 -- Aaron M. Ucko <email address hidden>  Sat, 14 Sep 2013 23:16:12 -0400
Superseded in jessie-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-5) unstable; urgency=low


  * demo/makeset.c: If unable to open an input ASN.1 file, report an error
    and exit rather than trying to work with a NULL pointer and crashing.
    (Thanks to Alexandre Rebert and the Mayhem Team at Carnegie Mellon
    University's Cylab for revealing this possibility.)
  * debian/control: Modernize libvibrant6b-dbg's short description.

 -- Aaron M. Ucko <email address hidden>  Thu, 27 Jun 2013 22:23:19 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-4) unstable; urgency=low


  * Rename libvibrant6(-dbg) to libvibrant6b(-dbg), as the release team
    doesn't condone ever reusing binary package names.
  * blast2: Conflict with unofficial ncbi-blast packages.  (LP: #658240.)
  * Rebuild in a clean environment.  (Closes: #714070.)

 -- Aaron M. Ucko <email address hidden>  Tue, 25 Jun 2013 22:00:52 -0400

Available diffs

Superseded in sid-release 
ncbi-tools6 (6.1.20120620-3) unstable; urgency=low


  * Migrate from Lesstif to Motif, which is (finally!) free these days.
    - Substitute libmotif-dev for liblesstif-dev in Build-Depends and
      libvibrant6-dev's Depends.
    - Rename libvibrant6a(-dbg) back to libvibrant6(-dbg).
  * Standards-Version: 3.9.4.  (Already compliant.)

 -- Aaron M. Ucko <email address hidden>  Tue, 28 May 2013 22:26:01 -0400
Superseded in jessie-release
Published in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20120620-2) unstable; urgency=low


  [ Andreas Tille ]
  * debian/upstream: Strings containing ': ' need to be quoted.

 -- Aaron M. Ucko <email address hidden>  Sun, 24 Jun 2012 22:54:29 -0400

Available diffs

Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20110713-6) unstable; urgency=low


  * debian/rules: Tweak -fPIC -> -fPIE substitution to accommodate platforms
    (kFreeBSD, and some Linux architectures) lacking PIE support.

 -- Aaron M. Ucko <email address hidden>  Fri, 01 Jun 2012 21:02:58 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20110713-5) unstable; urgency=low


  [ Andreas Tille ]
  * debian/upstream: Added citation information

  [ Aaron M. Ucko ]
  * debian/control:
    - Build-Depends-Indep: dpkg-dev (>= 1.16.2~) for dpkg-deb -Sextreme.
    - Repoint Vcs-* at anonscm.debian.org (vs. git.debian.org).
  * debian/rules:
    - Enable full hardening flags, contriving to substitute -fPIC for
      -fPIE as necessary.
    - Build ncbi-rrna-data with -Sextreme rather than hacking XZ_OPT.
  * make/makeshlb.unx: Honor externally supplied (hardening) LDFLAGS.
  
 -- Aaron M. Ucko <email address hidden>  Fri, 01 Jun 2012 18:36:37 -0400
Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20110713-4) unstable; urgency=low


  * debian/control:
    - Give ncbi-rrna-data a pre-dependency on dpkg (>= 1.15.6) for xz support.
    - Wrap and sort (build) dependencies.
    - Drop specific build dependency on libpng12-dev, even as a preferred
      libpng-dev provider.  (Closes: #662442.)
    - Require debhelper (>= 9), which has been final for some time.
    - Standards-Version: 3.9.3.  (No changes needed.)
  * debian/{libncbi6,ncbi-tools-bin}.install: sort as well.

 -- Aaron M. Ucko <email address hidden>  Thu, 08 Mar 2012 19:14:20 -0500
Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20110713-3) unstable; urgency=low


  * debian/{libncbi6-dev,ncbi-tools-bin}.install: move /usr/bin/asntool
    and /usr/bin/errhdr from libncbi6-dev to ncbi-tools-bin so that the
    former can properly be Multi-Arch: same.  (Closes: #646970.)
  * debian/libncbi6-dev.NEWS.debian: note the above move.
  * debian/control: adjust descriptions and relationships accordingly.
  * debian/{libncbi6-dev,ncbi-tools-bin}.lintian-overrides: update accordingly.
  * debian/rules:
    - Don't try to give libncbi6-dev manpages or menu entries.
    - Compress the giant ncbi-rrna-data package with xz -7e (the sweet spot).
  
 -- Aaron M. Ucko <email address hidden>  Sun, 30 Oct 2011 20:52:57 -0400
Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20110713-2) unstable; urgency=low


  * api/alignmgr2.c, api/pgppop.c, api/txalign.c, desktop/seqpanel.c,
    tools/spidey.c: avoid calling printf and the like with non-constant
    strings, as caught by -Werror=format-security.  (Closes: #643444.)

 -- Aaron M. Ucko <email address hidden>  Sat, 01 Oct 2011 22:08:13 -0400
Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20110713-1) unstable; urgency=low


  * New upstream release.
  * debian/*.symbols: update accordingly.
  * make/makeshlb.unx: link libcn3dOGL.so against -lm for sqrt.
  * doc/man/*.1: update for new release.
  * debian/rules:
    - (VIB): add asnmacro, as upstream takes care to publish binaries thereof.
    - Retire obsolete multiarch-unaware checks for libpthread.
    - Fully modernize Debhelper usage; in particular, transition to overrides.
  * debian/compat: advance to 9 per rules modernization.
  * debian/ncbi-tools-bin.install: add asnmacro.
  * make/makenet.unx: link asnmacro only against libraries it directly needs.
  * doc/man/asnmacro.1: give asnmacro a man page.
  * doc/man/Psequin.1: list it in SEE ALSO.
  * network/id1arch/idfetch.c: revert redundant change (from #295110).
  * Convert to multiarch.
    - debian/rules: Install libraries (and ncbithr.o) to multiarch directories.
    - debian/lib*.install: match multiarch library paths.
    - debian/control:
      + Build-Depends: debhelper (>= 8.1.3~), implying a recent dpkg-dev.
      + Set Multi-Arch: as appropriate across the board, and specify
        Pre-Depends: ${misc:Pre-Depends} for runtime libraries.
  * debian/*.lintian-overrides: drop leading slashes for Lintian 2.5.x.
  * debian/control: Standards-Version: 3.9.2 (already compliant).

 -- Aaron M. Ucko <email address hidden>  Mon, 05 Sep 2011 18:55:02 -0400
Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20100808-3) unstable; urgency=low
  * vibrant/shim3d.c: support libpng 1.5+, per Nobuhiro Iwamatsu's most    helpful patch.  (Closes: #636006.) -- Aaron M. Ucko <email address hidden>  Sat, 30 Jul 2011 11:51:21 -0400
Superseded in wheezy-release
Superseded in sid-release 
ncbi-tools6 (6.1.20100808-2) unstable; urgency=low
  * Reupload to unstable following the release of Debian 6.0 (squeeze). -- Aaron M. Ucko <email address hidden>  Sun, 13 Feb 2011 15:07:22 -0500
Superseded in wheezy-release
Published in squeeze-release
Superseded in sid-release 
ncbi-tools6 (6.1.20090809-2) unstable; urgency=low


  * debian/rules
    - Clean up compilation settings; in particular, use dpkg-buildflags rather
      than relying on dpkg-buildpackage to have set CFLAGS appropriately.
    - (clean): restore expected empty directories if necessary,
      for compatibility with VCSes (notably git) that don't track them.
    - (VIB): add asndisc, as upstream takes care to publish binaries thereof.
  * debian/ncbi-tools6.install: likewise add asndisc.
  * (debian/).gitignore: Ignore content generated during build.
  * make/makenet.unx: don't link asndisc against extraneous libraries.
  * doc/man/asndisc.1: throw together a man page for asndisc.
  * doc/man/cleanasn.1: fix SEE ALSO formatting.
  * debian/control:
    - bump dpkg-dev build-dep to >= 1.15.7 for dpkg-buildflags.
    - Standards-Version: 3.9.1 (already compliant).
    - note switch to git-mediated Debian-Med team maintenance.

 -- Aaron M. Ucko <email address hidden>  Wed, 13 Oct 2010 20:23:37 -0400
Deleted in experimental-release (Reason: None provided.) 
ncbi-tools6 (6.1.20100808-1) experimental; urgency=low


  * New upstream release; the upgrade to BLAST 2.2.24 (from 2.2.21) should
    address a formatdb regression.  (LP: #586219.)
  * Uploading to experimental because squeeze is frozen.
  * debian/rules
    - Clean up compilation settings; in particular, use dpkg-buildflags rather
      than relying on dpkg-buildpackage to have set CFLAGS appropriately.
    - (clean): restore expected empty directories if necessary,
      for compatibility with VCSes (notably git) that don't track them.
    - (install-indep-stamp): adapt to new ncbilogo.ico contents.
    - (VIB): add asndisc, as upstream takes care to publish binaries thereof.
  * debian/ncbi-tools6.install: likewise add asndisc.
  * (debian/).gitignore: Ignore content generated during build.
  * debian/lib{ncbi6,vibrant6a}.symbols: update for latest release.
  * make/makenet.unx: don't link asndisc against extraneous libraries.
  * doc/man/*.1: update for latest release.
  * doc/man/asndisc.1: throw together a man page for asndisc.
  * doc/man/cleanasn.1: fix SEE ALSO formatting.
  * debian/control:
    - bump dpkg-dev build-dep to >= 1.15.7 for dpkg-buildflags.
    - Standards-Version: 3.9.1 (already compliant).
    - note switch to git-mediated Debian-Med team maintenance.

 -- Aaron M. Ucko <email address hidden>  Fri, 03 Sep 2010 17:43:17 -0400
Superseded in squeeze-release
Superseded in sid-release 
ncbi-tools6 (6.1.20090809-1) unstable; urgency=low


  * New upstream release.
  * debian/libncbi6.symbols: update accordingly.
  * debian/control: clean up obsolete or redundant relationship declarations.

 -- Aaron M. Ucko <email address hidden>  Tue, 11 Aug 2009 22:03:47 -0400
Superseded in sid-release 
ncbi-tools6 (6.1.20090719-1) unstable; urgency=low


  * New upstream release.
  * debian/lib{ncbi6,vibrant6a}.symbols: update accordingly.
  * doc/man/*.1: update accordingly as well.
  * debian/control: declare compliance with Policy 3.8.2 (no changes needed).

 -- Aaron M. Ucko <email address hidden>  Sat, 01 Aug 2009 21:19:49 -0400
Superseded in squeeze-release
Superseded in sid-release 
ncbi-tools6 (6.1.20090301-1) unstable; urgency=low


  * New upstream release; uploading to unstable now that lenny is out.
  * debian/lib{ncbi6,vibrant6a}.symbols: update accordingly.
  * doc/man/*.1: update accordingly as well.
  * debian/control: place lib*-dbg in the new debug section, per the
    current override file.
  * debian/control: declare compliance with Policy 3.8.1 (no changes needed).
  * api/aliread.c: merge in fix (from 6.1.20080302-4) to undefined use of
    sprintf caught by Kees Cook's scan.
  * debian/watch: belatedly update regex to recognize releases like the
    previous one ([6.1.]20081116a).

 -- Aaron M. Ucko <email address hidden>  Thu, 19 Mar 2009 10:17:26 -0400
Superseded in experimental-release 
ncbi-tools6 (6.1.20081116a-2) experimental; urgency=low


  * debian/control: per Lintian's advice, depend on ${misc:Depends} across
    the board, in case Debhelper ever populates it.
  * debian/{control,rules}: split newly added large BLAST databases into a
    new ncbi-rrna-data package to keep ncbi-data to a reasonable size.

 -- Aaron M. Ucko <email address hidden>  Wed, 17 Dec 2008 19:45:48 -0500
Superseded in squeeze-release
Published in lenny-release
Superseded in sid-release 
ncbi-tools6 (6.1.20080302-4) unstable; urgency=medium


  * doc/fwd_check.sh: use mktemp rather than predictable names (formally
    CVE-2008-5149).
  * api/aliread.c: fix undefined use of sprintf caught by Kees Cook's scan.

 -- Aaron M. Ucko <email address hidden>  Sun, 28 Dec 2008 20:31:00 -0500
Superseded in sid-release
Superseded in lenny-release 
ncbi-tools6 (6.1.20080302-3) unstable; urgency=high


  * tools/readdb.c: enable madvise()-based code on all glibc (hence all
    Debian) systems, not just Linux.  (Closes: #490437.)

 -- Aaron M. Ucko <email address hidden>  Mon, 14 Jul 2008 19:43:15 -0400
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