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
that is not perfect, since it would fix the latest upstream version only.
Well, this needs some further discussions ...
** Also affects: bedtools (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/1961427
Title:
zlib: compressBound() returns an incorrect result on z15
Status in Ubuntu on IBM z Systems:
Incomplete
Status in bedtools package in Ubuntu:
New
Status in zlib package in Ubuntu:
Incomplete
Status in bedtools source package in Focal:
New
Status in zlib source package in Focal:
New
Status in bedtools source package in Impish:
New
Status in zlib source package in Impish:
New
Status in bedtools source package in Jammy:
New
Status in zlib source package in Jammy:
Incomplete
Bug description:
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 adjusted for DFLTCC.
[Fix]
* Adjust compressBound() for DFLTCC like it's already done
for deflateBound().
* Since zlib project does not accept patches at the moment,
the fix has been integrated into the DFLTCC pull request:
https://github.com/madler/zlib/pull/410
The commitid is b25781e735363e04f6c56e21431c47e4afc50b17.
* The fix extracted out of the above is:
https://launchpadlibrarian.net/589857296/debdiff_zlib_1.2.11.dfsg-2ubuntu7_to_zlib_1.2.11.dfsg-2ubuntu8_jammy.diff
[Test Plan]
* An IBM z15 system (LPAR, z/VM guest or KVM virtual machine)
with Ubuntu Server 21.10 (or 22.04).
* A test can be done based on the following C test program:
#include <assert.h>
#include <stdlib.h>
#include <zlib.h>
int main() {
Bytef in_buf[128], out_buf[1024];
for (size_t i = 0; i < sizeof(in_buf); i++)
in_buf[i] = rand();
uLongf dest_len = compressBound(sizeof(in_buf));
assert(dest_len <= sizeof(out_buf));
int ret = compress(out_buf, &dest_len,
in_buf, sizeof(in_buf));
assert(ret == Z_OK);
}
* The test needs to be done by IBM, due to the requirements
for the special z15 hardware.
* A successful test was just completed, based on the version in jammy-
proposed, which is at the same code level that the impish version this
SRU is targeted for.
[Where problems could occur]
* If the adjustment of compressBound() for DFLTCC is done
erroneously the issue can still be present or in worst case
even affect Z systems other than z15 only.
* The compression can become errorneous with the new changes,
e.g. in compressBound.
* Mistakes in dfltcc_free_window OF and especially DEFLATE_BOUND_COMPLEN,
(incl. the bit definitions), may cause various and unforseen defects.
* Any build time issues that might have been introduced by this patch
can be identified by a test build; this was done and is available here:
https://launchpad.net/~fheimes/+archive/ubuntu/lp1961427
[Other Info]
* Ubuntu jammy, impish and focal are affected.
__________
Description: zlib: compressBound() returns an incorrect result on z15
Symptom: Passing the result of compressBound() to compress()
results in an error code.
Problem: compressBound() is not adjusted for DFLTCC.
Solution: Adjust compressBound() for DFLTCC like it's already done
for deflateBound(). Since zlib project does not accept
patches at the moment, the fix has been integrated into
the DFLTCC pull request:
https://github.com/madler/zlib/pull/410
The commitid is b25781e735363e04f6c56e21431c47e4afc50b17.
Reproduction: z15 only:
#include <assert.h>
#include <stdlib.h>
#include <zlib.h>
int main() {
Bytef in_buf[128], out_buf[1024];
for (size_t i = 0; i < sizeof(in_buf); i++)
in_buf[i] = rand();
uLongf dest_len = compressBound(sizeof(in_buf));
assert(dest_len <= sizeof(out_buf));
int ret = compress(out_buf, &dest_len,
in_buf, sizeof(in_buf));
assert(ret == Z_OK);
}
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