| 2022-08-01 08:56:05 |
Frank Heimes |
bug |
|
|
added bug |
| 2022-08-01 09:04:50 |
Frank Heimes |
description |
samtools-legacy is the source package for libbam-dev,
which is used by libbio-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
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, but a bgzf_dopen instead etc. - looks
pretty much out of date), so it does not apply cleanly.
According to upstream 'https://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013. |
samtools-legacy is the source package for libbam-dev,
which is used by libbio-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
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one where the PR#1258 was designed for and that is used in the htslib or bedtools package (no bgzf_hopen - looks a bit out of date), so it does not apply cleanly.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://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013. |
|
| 2022-08-01 18:07:37 |
Frank Heimes |
attachment added |
|
debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5606313/+files/debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff |
|
| 2022-08-01 18:08:58 |
Frank Heimes |
samtools-legacy (Ubuntu): status |
New |
In Progress |
|
| 2022-08-01 20:25:27 |
Ubuntu Foundations Team Bug Bot |
tags |
kinetic s390x update-excuse |
kinetic patch s390x update-excuse |
|
| 2022-08-01 20:25:36 |
Ubuntu Foundations Team Bug Bot |
bug |
|
|
added subscriber Ubuntu Sponsors Team |
| 2022-08-03 12:33:10 |
Frank Heimes |
attachment removed |
debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5606313/+files/debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff |
|
|
| 2022-08-03 18:29:30 |
Frank Heimes |
attachment added |
|
debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5606801/+files/debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff |
|
| 2022-08-04 15:02:09 |
Olivier Gayot |
attachment added |
|
autopkgtest-logs https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5607043/+files/autopkgtest-logs.tar.xz |
|
| 2022-08-04 15:02:42 |
Olivier Gayot |
bug |
|
|
added subscriber Olivier Gayot |
| 2022-08-05 09:51:09 |
Olivier Gayot |
attachment added |
|
samtools-legacy_0.1.19+dfsg-5_0.1.19+dfsg-5ubuntu1.diff https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5607131/+files/samtools-legacy_0.1.19+dfsg-5_0.1.19+dfsg-5ubuntu1.diff |
|
| 2022-08-08 15:02:35 |
Frank Heimes |
attachment added |
|
debdiff_samtools-legacy_focal_from_0.1.19-4_to_0.1.19-4ubuntu0.1.diff https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5607373/+files/debdiff_samtools-legacy_focal_from_0.1.19-4_to_0.1.19-4ubuntu0.1.diff |
|
| 2022-08-08 15:02:51 |
Frank Heimes |
attachment added |
|
debdiff_libbio-samtools-perl_focal_from_1.43-2build1_to_1.43-2ubuntu0.1.diff https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5607374/+files/debdiff_libbio-samtools-perl_focal_from_1.43-2build1_to_1.43-2ubuntu0.1.diff |
|
| 2022-08-08 15:03:09 |
Frank Heimes |
tags |
kinetic patch s390x update-excuse |
focal kinetic patch s390x update-excuse |
|
| 2022-08-10 11:02:51 |
Frank Heimes |
description |
samtools-legacy is the source package for libbam-dev,
which is used by libbio-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
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://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013. |
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-samtools-perl.
* libbio-samtools-perl is linked to libbam-dev from samtools-legacy;
and samtools-legacy contains another bgzf.c implementation.
* Hence PR #1258 is needed to fix bgzf.c as part of samtools-legacy.
* And libbio-samtools-perl needs then rebuild to like against the
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).
* 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=proposed --apt-upgrade \
--shell-fail --setup-commands="apt -y -q install \
software-properties-common; apt-key adv --keyserver \
hkp://keyserver.ubuntu.com:80 --recv-keys \
73E9E91F16C43C45C621AE3EDF0A28DEFAFEB468; add-apt-repository -y \
ppa:fheimes/lp1983255; apt update; apt -y upgrade; apt install -y \
libbam-dev=0.1.19+dfsg-5ubuntu1" samtools-legacy_0.1.19+dfsg-5ubuntu1.dsc \
-- lxd autopkgtest/ubuntu/kinetic/s390x
(for focal and jammy adjust the versions accordingly)
* Without PR #1258 in place, the error: 'bgzf.c:<line-number>: bgzf_open:
Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE'
will occur.
* If the above test is successful one can rebuild 'libbio-samtools-perl',
and run the autopkgtest of 'libbio-samtools-perl' on top.
[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-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
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://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013. |
|
| 2022-08-10 14:00:58 |
Frank Heimes |
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-samtools-perl.
* libbio-samtools-perl is linked to libbam-dev from samtools-legacy;
and samtools-legacy contains another bgzf.c implementation.
* Hence PR #1258 is needed to fix bgzf.c as part of samtools-legacy.
* And libbio-samtools-perl needs then rebuild to like against the
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).
* 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=proposed --apt-upgrade \
--shell-fail --setup-commands="apt -y -q install \
software-properties-common; apt-key adv --keyserver \
hkp://keyserver.ubuntu.com:80 --recv-keys \
73E9E91F16C43C45C621AE3EDF0A28DEFAFEB468; add-apt-repository -y \
ppa:fheimes/lp1983255; apt update; apt -y upgrade; apt install -y \
libbam-dev=0.1.19+dfsg-5ubuntu1" samtools-legacy_0.1.19+dfsg-5ubuntu1.dsc \
-- lxd autopkgtest/ubuntu/kinetic/s390x
(for focal and jammy adjust the versions accordingly)
* Without PR #1258 in place, the error: 'bgzf.c:<line-number>: bgzf_open:
Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE'
will occur.
* If the above test is successful one can rebuild 'libbio-samtools-perl',
and run the autopkgtest of 'libbio-samtools-perl' on top.
[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-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
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://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013. |
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-samtools-perl.
* libbio-samtools-perl is linked to libbam-dev from samtools-legacy;
and samtools-legacy contains another bgzf.c implementation.
* Hence PR #1258 is needed to fix bgzf.c as part of samtools-legacy.
* And libbio-samtools-perl needs then rebuild to like against the
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/lp1961427
* 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=proposed --apt-upgrade \
--shell-fail --setup-commands="apt -y -q install \
software-properties-common; apt-key adv --keyserver \
hkp://keyserver.ubuntu.com:80 --recv-keys \
73E9E91F16C43C45C621AE3EDF0A28DEFAFEB468; add-apt-repository -y \
ppa:fheimes/lp1983255; apt update; apt -y upgrade; apt install -y \
libbam-dev=0.1.19+dfsg-5ubuntu1" samtools-legacy_0.1.19+dfsg-5ubuntu1.dsc \
-- lxd autopkgtest/ubuntu/kinetic/s390x
(for focal and jammy adjust the versions accordingly)
* Without PR #1258 in place, the error: 'bgzf.c:<line-number>: bgzf_open:
Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE'
will occur.
* If the above test is successful one can rebuild 'libbio-samtools-perl',
and run the autopkgtest of 'libbio-samtools-perl' on top.
[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-samtools-perl (autopkgtests),
that is for example triggered by a zlib update (proposed-transition).
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://github.com/lh3/samtools-legacy' the project
is "For testing only." and marked as "DON'T USE!" and it's last update
is from Nov 9, 2013. |
|
| 2022-08-11 07:07:54 |
Lukas Märdian |
nominated for series |
|
Ubuntu Kinetic |
|
| 2022-08-11 07:07:54 |
Lukas Märdian |
bug task added |
|
samtools-legacy (Ubuntu Kinetic) |
|
| 2022-08-11 07:07:54 |
Lukas Märdian |
nominated for series |
|
Ubuntu Focal |
|
| 2022-08-11 07:07:54 |
Lukas Märdian |
bug task added |
|
samtools-legacy (Ubuntu Focal) |
|
| 2022-08-11 07:07:54 |
Lukas Märdian |
nominated for series |
|
Ubuntu Jammy |
|
| 2022-08-11 07:07:54 |
Lukas Märdian |
bug task added |
|
samtools-legacy (Ubuntu Jammy) |
|
| 2022-08-11 07:14:20 |
Lukas Märdian |
samtools-legacy (Ubuntu Kinetic): status |
In Progress |
Fix Committed |
|
| 2022-08-11 07:33:55 |
Olivier Gayot |
attachment added |
|
1-1.43-3build2__1.43-3build3.debdiff https://bugs.launchpad.net/ubuntu/kinetic/+source/samtools-legacy/+bug/1983255/+attachment/5607809/+files/1-1.43-3build2__1.43-3build3.debdiff |
|
| 2022-08-11 07:35:30 |
Olivier Gayot |
bug task added |
|
libbio-samtools-perl (Ubuntu) |
|
| 2022-08-11 08:00:07 |
Lukas Märdian |
samtools-legacy (Ubuntu Jammy): status |
New |
In Progress |
|
| 2022-08-11 08:12:22 |
Lukas Märdian |
samtools-legacy (Ubuntu Focal): status |
New |
In Progress |
|
| 2022-08-12 01:21:39 |
Launchpad Janitor |
samtools-legacy (Ubuntu Kinetic): status |
Fix Committed |
Fix Released |
|
| 2022-08-12 07:59:23 |
Simon Chopin |
libbio-samtools-perl (Ubuntu Kinetic): status |
New |
Fix Committed |
|
| 2022-08-13 02:08:21 |
Launchpad Janitor |
libbio-samtools-perl (Ubuntu Kinetic): status |
Fix Committed |
Fix Released |
|
| 2022-08-20 00:26:32 |
Steve Langasek |
samtools-legacy (Ubuntu Jammy): status |
In Progress |
Fix Committed |
|
| 2022-08-20 00:26:34 |
Steve Langasek |
bug |
|
|
added subscriber Ubuntu Stable Release Updates Team |
| 2022-08-20 00:26:36 |
Steve Langasek |
bug |
|
|
added subscriber SRU Verification |
| 2022-08-20 00:26:38 |
Steve Langasek |
tags |
focal kinetic patch s390x update-excuse |
focal kinetic patch s390x update-excuse verification-needed verification-needed-jammy |
|
| 2022-08-20 00:28:26 |
Steve Langasek |
samtools-legacy (Ubuntu Focal): status |
In Progress |
Fix Committed |
|
| 2022-08-20 00:28:34 |
Steve Langasek |
tags |
focal kinetic patch s390x update-excuse verification-needed verification-needed-jammy |
focal kinetic patch s390x update-excuse verification-needed verification-needed-focal verification-needed-jammy |
|
| 2022-08-20 00:29:14 |
Steve Langasek |
removed subscriber Ubuntu Sponsors Team |
|
|
|
| 2022-08-20 00:29:25 |
Steve Langasek |
bug |
|
|
added subscriber Ubuntu Sponsors Team |
| 2022-08-20 19:37:52 |
Frank Heimes |
tags |
focal kinetic patch s390x update-excuse verification-needed verification-needed-focal verification-needed-jammy |
focal kinetic patch s390x update-excuse verification-done-jammy verification-needed verification-needed-focal |
|
| 2022-08-20 19:39:07 |
Frank Heimes |
tags |
focal kinetic patch s390x update-excuse verification-done-jammy verification-needed verification-needed-focal |
focal kinetic patch s390x update-excuse verification-done verification-done-focal verification-done-jammy |
|
| 2022-08-20 19:47:24 |
Frank Heimes |
attachment added |
|
debdiff libbio-samtools-perl focal from 1.43-2build1 to 1.43-2build2 https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5610297/+files/debdiff_libbio-samtools-perl_focal_from_1.43-2build1_to_1.43-2build2.diff |
|
| 2022-08-20 19:48:21 |
Frank Heimes |
attachment added |
|
debdiff libbio-samtools-perl jammy from 1.43-3build2 to 1.43-3build3 https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5610298/+files/debdiff_libbio-samtools-perl_jammy_from_1.43-3build2_to_1.43-3build3.diff |
|
| 2022-08-22 09:52:11 |
Lukas Märdian |
libbio-samtools-perl (Ubuntu Jammy): status |
New |
In Progress |
|
| 2022-08-22 09:56:41 |
Lukas Märdian |
libbio-samtools-perl (Ubuntu Focal): status |
New |
In Progress |
|
| 2022-08-22 09:56:43 |
Lukas Märdian |
removed subscriber Ubuntu Sponsors Team |
|
|
|
| 2022-08-22 10:13:59 |
Łukasz Zemczak |
libbio-samtools-perl (Ubuntu Focal): status |
In Progress |
Fix Committed |
|
| 2022-08-22 10:14:05 |
Łukasz Zemczak |
tags |
focal kinetic patch s390x update-excuse verification-done verification-done-focal verification-done-jammy |
focal kinetic patch s390x update-excuse verification-done-jammy verification-needed verification-needed-focal |
|
| 2022-08-22 10:51:00 |
Łukasz Zemczak |
libbio-samtools-perl (Ubuntu Jammy): status |
In Progress |
Fix Committed |
|
| 2022-08-22 10:51:05 |
Łukasz Zemczak |
tags |
focal kinetic patch s390x update-excuse verification-done-jammy verification-needed verification-needed-focal |
focal kinetic patch s390x update-excuse verification-needed verification-needed-focal verification-needed-jammy |
|
| 2022-08-25 10:05:24 |
Frank Heimes |
tags |
focal kinetic patch s390x update-excuse verification-needed verification-needed-focal verification-needed-jammy |
focal kinetic patch s390x update-excuse verification-done-jammy verification-needed verification-needed-focal |
|
| 2022-09-05 07:51:03 |
Launchpad Janitor |
samtools-legacy (Ubuntu Jammy): status |
Fix Committed |
Fix Released |
|
| 2022-09-05 07:51:06 |
Launchpad Janitor |
libbio-samtools-perl (Ubuntu Jammy): status |
Fix Committed |
Fix Released |
|
| 2022-09-05 07:51:09 |
Łukasz Zemczak |
removed subscriber Ubuntu Stable Release Updates Team |
|
|
|
| 2022-09-05 11:15:06 |
Frank Heimes |
tags |
focal kinetic patch s390x update-excuse verification-done-jammy verification-needed verification-needed-focal |
focal kinetic patch s390x update-excuse verification-done verification-done-focal verification-done-jammy |
|
| 2022-09-12 14:43:52 |
Launchpad Janitor |
samtools-legacy (Ubuntu Focal): status |
Fix Committed |
Fix Released |
|
| 2022-09-12 14:43:56 |
Launchpad Janitor |
libbio-samtools-perl (Ubuntu Focal): status |
Fix Committed |
Fix Released |
|
| 2022-09-12 15:24:19 |
Frank Heimes |
bug task added |
|
ubuntu-z-systems |
|
| 2022-09-12 15:24:27 |
Frank Heimes |
ubuntu-z-systems: status |
New |
Fix Released |
|
