Sync bedtools 2.31.1+dfsg-2 (universe) from Debian unstable (main)
| Affects | Status | Importance | Assigned to | Milestone | |
|---|---|---|---|---|---|
| bedtools (Ubuntu) |
Fix Released
|
Wishlist
|
Unassigned | ||
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-
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+
bedtools (2.31.1+dfsg-2) unstable; urgency=medium
* d/clean: new: remove test/getfasta/
-- Étienne Mollier <email address hidden> 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 <email address hidden> 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 <email address hidden> 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_
* 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 <email address hidden> 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 <email address hidden> Thu, 13 Apr 2023 14:12:15 +0200
| Changed in bedtools (Ubuntu): | |
| importance: | Undecided → Wishlist |
| Athos Ribeiro (athos-ribeiro) wrote | #1 |
| Changed in bedtools (Ubuntu): | |
| status: | New → Fix Released |
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/
-- Étienne Mollier <email address hidden> 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 <email address hidden> 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 <email address hidden> 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_
* 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 <email address hidden> 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 <email address hidden> Thu, 13 Apr 2023 14:12:15 +0200