samtools-legacy misses 'Remove compressBound assertions' (PR #1258) fix
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
Ubuntu on IBM z Systems |
Fix Released
|
Undecided
|
Unassigned | ||
libbio-samtools-perl (Ubuntu) |
Fix Released
|
Undecided
|
Unassigned | ||
Focal |
Fix Released
|
Undecided
|
Unassigned | ||
Jammy |
Fix Released
|
Undecided
|
Unassigned | ||
Kinetic |
Fix Released
|
Undecided
|
Unassigned | ||
samtools-legacy (Ubuntu) |
Fix Released
|
High
|
Unassigned | ||
Focal |
Fix Released
|
Undecided
|
Unassigned | ||
Jammy |
Fix Released
|
Undecided
|
Unassigned | ||
Kinetic |
Fix Released
|
High
|
Unassigned |
Bug Description
SRU Justification:
==================
[Impact]
* zlib requires a fix for 'compressBound() returns an incorrect result
on z15' (described at LP#1961427 in more detail).
* But the above patch expects that another fix 'Remove compressBound
assertions' (PR #1258) is in place for all bgzf.c implementations.
* The packages htslib and bedtools are covered in LP#1961427.
* Unfortunately more 'embedded' or better 'bundled' bgzf.c implementations
exist, that are difficult to find upfront, hence the zlib proposed migration
now pointed to libbio-
* libbio-
and samtools-legacy contains another bgzf.c implementation.
* Hence PR #1258 is needed to fix bgzf.c as part of samtools-legacy.
* And libbio-
fixed libbam-dev.
* PR #1258 removes the Assert lines and modifies bgzf_compress.
[Test Plan]
* An IBM zSystem (LPAR, z/VM guest or KVM virtual machine)
with Ubuntu Server 20.04 (or 22.04 or 22.10).
* Having the zlib version from -proposed installed or from PPA:
ppa:fheimes/
* The easiest way to test this is based on the autopkgtest of the affected
package, here 'samtools-legacy' (here a manual autopkgtest execution):
autopkgtest --no-built-binaries --apt-pocket=
--shell-fail --setup-
software-
hkp:
73E9E91F1
ppa:
libbam-
-- lxd autopkgtest/
(for focal and jammy adjust the versions accordingly)
* Without PR #1258 in place, the error: 'bgzf.c:
Assertion `compressBound(
will occur.
* If the above test is successful one can rebuild 'libbio-
and run the autopkgtest of 'libbio-
[Where problems could occur]
* The bgzf.c implementation as it is in 'samtools-legacy' is very outdated
and the code was not touched for close to 10 years.
* Hence PR #1258 could not directly be applied, and a backport was needed.
* Issues could be that checks (due to missing asserts) are now insufficient,
* or (un-)compress does not work properly anymore, due to the changes in
bgzf_compress.
* But the autopkgtest(s) will be helpful to ensure proper functionality.
[Other Info]
* The different bgzf.c versions that are bundled are almost all
slightly different implementations, hence the backport of PR #1258
needs to be a bit adjusted here and there.
__________
samtools-legacy is the source package for libbam-dev,
which is used by libbio-
that is for example triggered by a zlib update (proposed-
zlib requires a fix for 'compressBound() returns an incorrect result on z15' LP#1961427 that again requires the 'Remove compressBound assertions' (PR #1258) fix in all bgzf.c implementations, like htslib, bedtools or even samtools-legacy.
Problematic is that the code differs quite a bit from the one where the PR#1258 was designed for and that is used in the htslib or bedtools package (no bgzf_hopen - looks a bit out of date), so it does not apply cleanly.
According to upstream 'https:/
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013.
description: | updated |
description: | updated |
description: | updated |
Changed in libbio-samtools-perl (Ubuntu Kinetic): | |
status: | New → Fix Committed |
Changed in ubuntu-z-systems: | |
status: | New → Fix Released |
I've created a backport of PR #1258 that applied to bgzf.c from samtools-legacy. /launchpad. net/~fheimes/ +archive/ ubuntu/ lp1983255
I did a PPA test build: https:/