--- Comment From i...@de.ibm.com 2022-09-05 11:31 EDT---
zlib1g-dev s390x 1:1.2.11.dfsg-2ubuntu9.1 and zlib1g s390x
1:1.2.11.dfsg-2ubuntu9.1 pass all of my tests.
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(While looking into libbio-samtools-perl and other related packages, I
found that there is yet another htslib bundled in tabix - which is not
great. But this at at least already the needed patch.)
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--- Comment From boris.m...@de.ibm.com 2022-07-21 05:51 EDT---
Comment on attachment 153124
zlib_1.2.11.dfsg-2ubuntu7_to_zlib_1.2.11.dfsg-2ubuntu8 (jammy)
this is obsolete - has been replaced by newer version
--- Comment From boris.m...@de.ibm.com 2022-07-21 05:52 EDT---
Comment
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.
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Due to the fact that now in total 3 packages are involved and two libraries
(zlib and htslib, well and the libraries included in bedtools), this will cause
a bigger transition (especially for htslib in focal, and zlib itself on all
affected Ubuntu releases).
(The transition(s) need to be
--- Comment From mario.h...@de.ibm.com 2022-07-07 07:55 EDT---
(In reply to comment #13)
> We just realized that we had DFLTCC support in 20.04, so we need to put this
> fix there as well.
So this still gets fixed in Focal (20.04).
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--- Comment From i...@de.ibm.com 2022-06-15 14:00 EDT---
I don't really remember, so I retested.
20.04: 1.2.11.dfsg-2ubuntu1.3 fixes the problem (I had to install the .deb file
manually with dpkg).
22.04: 1.2.11.dfsg-2ubuntu9.1 fixes the problem.
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--- Comment From i...@de.ibm.com 2022-05-16 06:17 EDT---
With the new combination, bedtools testsuite is green and zlib passes all of my
tests too. So it looks good, thanks!
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--- Comment From i...@de.ibm.com 2022-05-10 07:14 EDT---
Hi, thanks for looking into this. I'll wait until
https://launchpad.net/~fheimes/+archive/ubuntu/lp1961427 finishes the build and
try it.
In the meantime I've asked the bedtools upstream to cherry-pick the
htslib commit:
Well, that bundled htslib seems to make the situation a bit messy,
So my guess is that this should be fixed in bedtools upstream first...
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--- Comment From i...@de.ibm.com 2022-05-06 06:22 EDT---
Here are the originally reported failures:
> But I found in "bedtools":
> bedtools: bgzf.c:351: bgzf_hopen: Assertion
> `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE' failed. test-
> intersect.sh: line 201: 1981 Aborted
--- Comment From i...@de.ibm.com 2022-05-04 08:51 EDT---
Good that this was pinged - it seems that we hit a deadlock here :-)
I was waiting on Ubuntu to bump the HTSlib version (or cherry-pick
https://github.com/samtools/htslib/pull/1258), where the incompatibility
issue is resolved. The
--- Comment From mario.h...@de.ibm.com 2022-05-04 05:20 EDT---
It seems there is no progress with this issue for a while. What is next? Is the
reason for the incompatibility found meanwhile?
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--- Comment From i...@de.ibm.com 2022-03-15 18:41 EDT---
zlib1g s390x 1:1.2.11.dfsg-2ubuntu1.3 passes all of my tests on focal, thanks!
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