[Bug 2048088] Re: Sync bedtools 2.31.1+dfsg-2 (universe) from Debian unstable (main)

[Athos Ribeiro]

This bug was fixed in the package bedtools - 2.31.1+dfsg-2
Sponsored for Mate Kukri (mkukri)

---------------
bedtools (2.31.1+dfsg-2) unstable; urgency=medium

  * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957)

 -- Étienne Mollier <emollier at debian.org>  Mon, 04 Dec 2023 20:13:11
+0100

bedtools (2.31.1+dfsg-1) unstable; urgency=medium

  * New upstream version 2.31.1+dfsg
  * gcc-13.patch: remove: applied upstream.

 -- Étienne Mollier <emollier at debian.org>  Fri, 24 Nov 2023 12:10:46
+0100

bedtools (2.31.0+dfsg-2) unstable; urgency=medium

  * gcc-13.patch: fixed upstream by different change.
    The Applied-Upstream field is set accordingly to point to PR 1067.
  * d/rules: use sse for floating point calculations.
    This fixes bedtools "intersect" test failures during build time.
    This change is brought for consistency with htslib's own settings.
    While this is an architecture baseline violation, the alternative
    is no htslib support at all for the i386 distribution, since it
    fails its own test suite with anything else than sse for floating
    point calculations. (Closes: #1055414)
  * d/control: depend on python3:any per M-A hint.

 -- Étienne Mollier <emollier at debian.org>  Sat, 18 Nov 2023 16:34:59
+0100

bedtools (2.31.0+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.6.2 (routine-update)
  * remove_barski_binding_site.png.patch: unfuzz.
  * 2to3.patch: refresh.
  * 2to3.patch: declare forwarding not-needed.
    Upstream looks to assume compatibility with both python and python3.
  * 2to3.patch: remove further occurrences of python.
    There are some tests and some documentation referring to the
    unversioned python, which in Debian is by default python2.
  * hardening patch: unfuzz.
  * htsutil patch: unfuzz.
  * gcc-13.patch: add; fix ftbfs with gcc-13.
    Thanks to David Seifert (Closes: #1037588)
  * d/control: bedtools-test depend on python3.

 -- Étienne Mollier <emollier at debian.org>  Fri, 23 Jun 2023 22:57:16
+0200

bedtools (2.30.0+dfsg-3) unstable; urgency=medium

  * Do not use ulimit in test
    Closes: #1034349
  * Override false positive (see lintian bug #1017966)

 -- Andreas Tille <tille at debian.org>  Thu, 13 Apr 2023 14:12:15 +0200

** Changed in: bedtools (Ubuntu)
       Status: New => Fix Released

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https://bugs.launchpad.net/bugs/2048088

Title:
  Sync bedtools 2.31.1+dfsg-2 (universe) from Debian unstable (main)

Status in bedtools package in Ubuntu:
  Fix Released

Bug description:
  Please sync bedtools 2.31.1+dfsg-2 (universe) from Debian unstable
  (main)

  Explanation of the Ubuntu delta and why it can be dropped:
    * Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support
      of fixing 'zlib: compressBound() returns an incorrect result on z15'.
      (LP: #1961427)

  Ubuntu delta included upstream and in Debian.

  Sync would also fix current FTBFS.

  Changelog entries since current noble version 2.30.0+dfsg-2ubuntu1:

  bedtools (2.31.1+dfsg-2) unstable; urgency=medium

    * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957)

   -- Étienne Mollier <emollier at debian.org>  Mon, 04 Dec 2023 20:13:11
  +0100

  bedtools (2.31.1+dfsg-1) unstable; urgency=medium

    * New upstream version 2.31.1+dfsg
    * gcc-13.patch: remove: applied upstream.

   -- Étienne Mollier <emollier at debian.org>  Fri, 24 Nov 2023 12:10:46
  +0100

  bedtools (2.31.0+dfsg-2) unstable; urgency=medium

    * gcc-13.patch: fixed upstream by different change.
      The Applied-Upstream field is set accordingly to point to PR 1067.
    * d/rules: use sse for floating point calculations.
      This fixes bedtools "intersect" test failures during build time.
      This change is brought for consistency with htslib's own settings.
      While this is an architecture baseline violation, the alternative
      is no htslib support at all for the i386 distribution, since it
      fails its own test suite with anything else than sse for floating
      point calculations. (Closes: #1055414)
    * d/control: depend on python3:any per M-A hint.

   -- Étienne Mollier <emollier at debian.org>  Sat, 18 Nov 2023 16:34:59
  +0100

  bedtools (2.31.0+dfsg-1) unstable; urgency=medium

    * New upstream version
    * Standards-Version: 4.6.2 (routine-update)
    * remove_barski_binding_site.png.patch: unfuzz.
    * 2to3.patch: refresh.
    * 2to3.patch: declare forwarding not-needed.
      Upstream looks to assume compatibility with both python and python3.
    * 2to3.patch: remove further occurrences of python.
      There are some tests and some documentation referring to the
      unversioned python, which in Debian is by default python2.
    * hardening patch: unfuzz.
    * htsutil patch: unfuzz.
    * gcc-13.patch: add; fix ftbfs with gcc-13.
      Thanks to David Seifert (Closes: #1037588)
    * d/control: bedtools-test depend on python3.

   -- Étienne Mollier <emollier at debian.org>  Fri, 23 Jun 2023 22:57:16
  +0200

  bedtools (2.30.0+dfsg-3) unstable; urgency=medium

    * Do not use ulimit in test
      Closes: #1034349
    * Override false positive (see lintian bug #1017966)

   -- Andreas Tille <tille at debian.org>  Thu, 13 Apr 2023 14:12:15 +0200

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