This bug was fixed in the package htslib - 1.10.2-3ubuntu0.1
---
htslib (1.10.2-3ubuntu0.1) focal; urgency=medium
* Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support
of fixing 'zlib: compressBound() returns an incorrect result on z15'.
Due a fuzz 2 a
** Changed in: ubuntu-z-systems
Status: Fix Committed => Fix Released
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Title:
zlib: compressBound() returns an
This bug was fixed in the package zlib - 1:1.2.11.dfsg-2ubuntu1.4
---
zlib (1:1.2.11.dfsg-2ubuntu1.4) focal; urgency=medium
* d/p/410-lp1961427.patch ported from zlib #410, fixing
compressBound() with hw acceleration. LP: #1961427
Thanks to Ilya Leoshkevich .
In
** Tags removed: foundations-todo
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Title:
zlib: compressBound() returns an incorrect result on z15
Status in Ubuntu on
--- Comment From i...@de.ibm.com 2022-09-22 08:10 EDT---
zlib1g s390x 1:1.2.11.dfsg-2ubuntu1.4 passes all of my tests.
--- Comment From boris.m...@de.ibm.com 2022-09-22 08:18 EDT---
@Ilya: thanks a lot for your instant verification on focal!
With that, I am updating the tags /
** Tags removed: verification-done verification-done-focal
** Tags added: verification-needed verification-needed-focal
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Well, I had comment #11 in mind where the 1:1.2.11.dfsg-2ubuntu1.3 was
successfully verified on focal.
Meanwhile that version got overruled by a security update:
zlib (1:1.2.11.dfsg-2ubuntu1.3) focal-security; urgency=medium
and became 'already used', hence a new version was needed for this bug
** Tags removed: verification-needed verification-needed-focal
** Tags added: verification-done verification-done-focal
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Hey Frank! You switched the focal verification tags, but I do not see
any verification of the focal packages. Comment #65 only mentions
versions for jammy. Have the focal packages been tested in any way?
Switching back tags for focal.
** Tags removed: verification-done verification-done-focal
**
** Changed in: ubuntu-z-systems
Status: In Progress => Fix Committed
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Title:
zlib: compressBound() returns an
This bug was fixed in the package bedtools - 2.30.0+dfsg-2ubuntu0.1
---
bedtools (2.30.0+dfsg-2ubuntu0.1) jammy; urgency=medium
* Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support
of fixing 'zlib: compressBound() returns an incorrect result on z15'.
This bug was fixed in the package zlib - 1:1.2.11.dfsg-2ubuntu9.1
---
zlib (1:1.2.11.dfsg-2ubuntu9.1) jammy; urgency=medium
* d/p/410-lp1961427.patch ported from zlib #410, fixing
compressBound() with hw acceleration. LP: #1961427
Thanks to Ilya Leoshkevich .
In
** Tags added: foundations-todo
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Title:
zlib: compressBound() returns an incorrect result on z15
Status in Ubuntu on
Thx Iliya! (updating tag accordingly)
** Tags removed: verification-needed verification-needed-focal
verification-needed-jammy
** Tags added: verification-done verification-done-focal verification-done-jammy
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This bug was fixed in the package zlib - 1:1.2.11.dfsg-2ubuntu10
---
zlib (1:1.2.11.dfsg-2ubuntu10) kinetic; urgency=medium
* d/p/410-lp1961427.patch ported from zlib #410, fixing
compressBound() with hw acceleration. LP: #1961427
Thanks to Ilya Leoshkevich .
In
Hello bugproxy, or anyone else affected,
Accepted zlib into jammy-proposed. The package will build now and be
available at
https://launchpad.net/ubuntu/+source/zlib/1:1.2.11.dfsg-2ubuntu9.1 in a
few hours, and then in the -proposed repository.
Please help us by testing this new package. See
Hello bugproxy, or anyone else affected,
Accepted bedtools into jammy-proposed. The package will build now and be
available at
https://launchpad.net/ubuntu/+source/bedtools/2.30.0+dfsg-2ubuntu0.1 in
a few hours, and then in the -proposed repository.
Please help us by testing this new package.
The zlib patch is already waiting in Jammy's unapproved queue, so I'm
marking it "In Progress".
** Changed in: zlib (Ubuntu Jammy)
Status: New => In Progress
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Regarding zlib focal-proposed migration:
For libbio-samtools-perl it's the same situation like on kinetic.
samtools-legacy requires the PR #1258, and libbio-samtools-perl a rebuild (to
link against the new libbio-dev). See update-excuse bug LP#1983255.
On top vcftools misses the 'Remove
Hello bugproxy, or anyone else affected,
Accepted zlib into focal-proposed. The package will build now and be
available at
https://launchpad.net/ubuntu/+source/zlib/1:1.2.11.dfsg-2ubuntu1.4 in a
few hours, and then in the -proposed repository.
Please help us by testing this new package. See
Hello bugproxy, or anyone else affected,
Accepted htslib into focal-proposed. The package will build now and be
available at
https://launchpad.net/ubuntu/+source/htslib/1.10.2-3ubuntu0.1 in a few
hours, and then in the -proposed repository.
Please help us by testing this new package. See
Actually, somebody will need to manually retrigger the gdcm test with
the version of zlib in -proposed and I'll do that now.
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There is now a solution for LP#1983255.
Meanwhile I've noticed that gdcm is now flagged as a new regression for
zlib's proposed miration at 'update excuses' (was not the case before).
Found that this happened on Debian too:
Looks like libbam-dev is the reason for the libbio-samtools-perl regression
on s390x. libbam-dev is used by libbio-samtools-perl and build based on it's
source package samtools-legacy, which includes another version of bgzf,
that misses the 'Remove compressBound assertions' (PR #1258) fix.
zlib 1:1.2.11.dfsg-2ubuntu10 is stuck in kinetic-proposed for some time:
http://people.canonical.com/~ubuntu-archive/proposed-
migration/kinetic/update_excuses.html#zlib
https://wiki.ubuntu.com/ProposedMigration
Several of the initial regressions were due to timeouts and network
issues and are
I've noticed that the updated zlib for kinetic just landed in -proposed:
"zlib | 1:1.2.11.dfsg-2ubuntu10 | kinetic-proposed"
hence I'm updating the corresponding entry to Fix Committed.
** Changed in: zlib (Ubuntu)
Status: In Progress => Fix Committed
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I believe I've sponsored all the uploads necessary to see this bug
fixed.
** Changed in: bedtools (Ubuntu Jammy)
Assignee: (unassigned) => Brian Murray (brian-murray)
** Changed in: htslib (Ubuntu Focal)
Assignee: (unassigned) => Brian Murray (brian-murray)
** Changed in: zlib (Ubuntu
This bug was fixed in the package bedtools - 2.30.0+dfsg-2ubuntu1
---
bedtools (2.30.0+dfsg-2ubuntu1) kinetic; urgency=medium
* Add d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support
of fixing 'zlib: compressBound() returns an incorrect result on z15'.
zlib debdiffs for kinetic, jammy and focal (latest, with proper dep3)
** Patch removed: "zlib debdiffs for jammy and kinetic (latest)"
https://bugs.launchpad.net/ubuntu/+source/htslib/+bug/1961427/+attachment/5604504/+files/debdiffs_J_K.tar.gz
** Attachment added: "zlib debdiffs for kinetic,
Since the zlib package progressed meanwhile due to a security update, I
created new debdiffs for jammy and kinetic - see debdiffs_J_K.tar.gz.
** Attachment added: "zlib debdiffs for jammy and kinetic (latest)"
** Attachment removed: "reverse dependencies, gathered on focal.txt"
https://bugs.launchpad.net/ubuntu/+source/zlib/+bug/1961427/+attachment/5597497/+files/reverse%20dependencies%2C%20gathered%20on%20focal.txt
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** Tags removed: targetmilestone-inin2110
** Tags added: targetmilestone-inin20045
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Title:
zlib: compressBound()
Just to clarify - only 21.10/impish got dropped.
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Title:
zlib: compressBound() returns an incorrect result on z15
You are right, these are 'just' fixes w/o ABI changes and I am not aware
(couldn't find) of any cases of static linkages - I apologize.
So fortunately the complexity of this will be far less.
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I'm just watching from the sidelines here, but why do we need to have
a transition for this? Is there an ABI break I'm not aware of? Or is zlib
usually statically linked in Debian packages?
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Thx for the retest!
With that I would go from Incomplete back to In Progress ...
** Changed in: ubuntu-z-systems
Status: Incomplete => In Progress
** Changed in: zlib (Ubuntu)
Status: Incomplete => In Progress
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I would like to proceed on this (to not loose to much time...)
To sum things up:
On top of the actual zlib fix,
there is another patch 'Remove compressBound assertions. (PR #1258)'
needed for htslib.
Unfortunately there is a standalone 'htslib' package,
as well as a htslib version included in
** Patch added:
"debdiff_bedtools_jammy_from_2.30.0+dfsg-2_to_2.30.0+dfsg-2ubuntu0.1.patch"
https://bugs.launchpad.net/ubuntu/focal/+source/bedtools/+bug/1961427/+attachment/5597489/+files/debdiff_bedtools_jammy_from_2.30.0+dfsg-2_to_2.30.0+dfsg-2ubuntu0.1.patch
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** Patch added:
"debdiff_bedtools_impish_from_2.30.0+dfsg-1_to_2.30.0+dfsg-1ubuntu0.1.patch"
https://bugs.launchpad.net/ubuntu/focal/+source/bedtools/+bug/1961427/+attachment/5597490/+files/debdiff_bedtools_impish_from_2.30.0+dfsg-1_to_2.30.0+dfsg-1ubuntu0.1.patch
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** Patch added:
"debdiff_bedtools_kinetic_from_2.30.0+dfsg-2_to_2.30.0+dfsg-2ubuntu1.patch"
https://bugs.launchpad.net/ubuntu/focal/+source/bedtools/+bug/1961427/+attachment/5597488/+files/debdiff_bedtools_kinetic_from_2.30.0+dfsg-2_to_2.30.0+dfsg-2ubuntu1.patch
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** 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.
* This is because compressBound() is not
Thx Ilya, restarted to work on this by adding updated bedtools to the
PPA ...
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Title:
zlib: compressBound() returns an
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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@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:
** 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:
** 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:
** 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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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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