Thx Ilya, restarted to work on this by adding updated bedtools to the
PPA ...
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Title:
zlib: compressBound() returns an incorrect result on z15
Just for the records: the standalone htslib package 1.13+ds-2build1 in jammy
includes PR-1258 already.
(and the PPA build is finished)
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Title:
@xnox Well, initially I was also a bit puzzled noticing that not the standalone
htslib is used, but an embedded htslib in bedtools.
But this is also upstream the case and htslib is not the only component that is
bundled:
$ ls ./src/utils/
BamToolsBlockedIntervals fileType
Usually we try to avoid using embedded copies of code. Is it at all
possible to convert some of the affected packages to use/reuse a shared
library instead?
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Ok, thx.
(and yes, the builders are currently a bit busy - just noticed the 140 jobs in
the queue ...
guess it's a matter of maybe 2+ hours ...)
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So, I've now created an updated bedtools package for jammy (having patched the
bundled htslib with 515f6df-Remove-compressBound-assertions.-PR-1258.patch) for
jammy,
and since the zlib package received some CVE patches meanwhile, I also created
a new patched zlib version (that incl.
That bundled htslib seems to make the situation a bit messy,
since bedtools does not clearly list the htslib version that was bundled or I
can't find it (oh, maybe it's 1.9) and the commit does not apply cleanly.
So my guess is that this should be fixed in bedtools upstream first... but even
Good to have this follow-up, indeed ...
(For a fix in htslib either a new LP bug is needed or htslib needs to be added
to this one as 'affecting package'.)
So I did some investigations and found that the "Remove compressBound
assertions." merge request #1258 got upstream accepted with htslib
We are waiting on Ilya (iii-i) for a refined patch.
He mentioned that this can take a while ...
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Title:
zlib: compressBound() returns an
** Changed in: zlib (Ubuntu Jammy)
Status: In Progress => Incomplete
** Changed in: ubuntu-z-systems
Status: New => Incomplete
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Currently dropping 1:1.2.11.dfsg-2ubuntu8 from jammy-proposed per the
uploader's request:
09:55 < fheimes> Dear ubuntu-release team, could you please drop/remove zlib
2.11.dfsg-2ubuntu8 from jammy-proposed (LP#1961427)?
09:55 < fheimes> An incompatibility with HTSlib was detected, I'm in contact
Sorry, the impish version needs to be of course "1.2.11.dfsg-2ubuntu7.1" - to
keep the upgrade path working.
Here is the updated debdiff
(debdiff_zlib_1.2.11.dfsg-2ubuntu7_to_zlib_1.2.11.dfsg-2ubuntu7.1_impish.diff).
** Patch removed:
And - just for the reason of completeness - the debdiff for impish, that
is equal to the jammy debdiff, except the release name at the top line
in the changelog
(debdiff_zlib_1.2.11.dfsg-2ubuntu7_to_zlib_1.2.11.dfsg-2ubuntu8).
** Patch added:
The patch applies cleanly not only to the impish and jammy versions, but
also to the focal version of zlib.
To be on the save side I did another test build for focal:
https://launchpad.net/~fheimes/+archive/ubuntu/lp1961427
And here is the focal debdiff attached
Let me check if the patch applies to the focal version, too.
A separate debdiff is needed for focal anyway.
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Title:
zlib: compressBound()
** Also affects: zlib (Ubuntu Focal)
Importance: Undecided
Status: New
** Description changed:
SRU Justification:
==
[Impact]
* zlib: compressBound() returns an incorrect result on IBM z15 hardware.
* Passing the result of compressBound() to
We just realized that we had DFLTCC support in 20.04, so we need to put
this fix there as well.
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Title:
zlib: compressBound() returns an
** Description changed:
SRU Justification:
==
[Impact]
* zlib: compressBound() returns an incorrect result on IBM z15 hardware.
* Passing the result of compressBound() to compress() results
- in an error code.
+ in an error code.
* This is because
SRU justification provides and added to the bug description.
** Description changed:
+ SRU Justification:
+ ==
+
+ [Impact]
+
+ * zlib: compressBound() returns an incorrect result on IBM z15 hardware.
+
+ * Passing the result of compressBound() to compress() results
+ in an
If this needs SRU'ing to impish please update the bug description
accordingly. I've sponsored this for Jammy.
** Changed in: zlib (Ubuntu Jammy)
Status: New => In Progress
** Changed in: zlib (Ubuntu Jammy)
Assignee: Skipper Bug Screeners (skipper-screen-team) => Brian Murray
** Changed in: zlib (Ubuntu Impish)
Importance: Undecided => High
** Changed in: zlib (Ubuntu Jammy)
Importance: Undecided => High
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Title:
The attachment "zlib_1.2.11.dfsg-2ubuntu7_to_zlib_1.2.11.dfsg-2ubuntu8
(jammy)" seems to be a debdiff. The ubuntu-sponsors team has been
subscribed to the bug report so that they can review and hopefully
sponsor the debdiff. If the attachment isn't a patch, please remove the
"patch" flag from
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