samtools-legacy misses 'Remove compressBound assertions' (PR #1258) fix

I've created a backport of PR #1258 that applied to bgzf.c from samtools-legacy.
I did a PPA test build: https://launchpad.net/~fheimes/+archive/ubuntu/lp1983255

The attachment "debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff" 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 the attachment, remove the "patch" tag, and if you are member of the ~ubuntu-sponsors, unsubscribe the team.

[This is an automated message performed by a Launchpad user owned by ~brian-murray, for any issue please contact him.]

Hi @fheimes!
I stumbled upon this bug when looking at proposed-migrations (i.e., zlib vs libbio-samtools-perl).

I ran autopkgtest on s390x against proposed and pinned libbam-dev to the version in your ppa (https://launchpad.net/~fheimes/+archive/ubuntu/lp1983255) but unfortunately the test is still red for me.

Would you mind having a quick glance and let me know if you think I overlooked or missed something?

I'm attaching the logs.

Best regards,
Olivier

It turned out that libbio-samtools-perl is statically linked to libbam-dev, hence libbio-samtools-perl needs a rebuild, too.
So with these two it seems to work:
ppa:fheimes/samtools-legacy
ppa:fheimes/libbio-samtools-perl
My local autopkgtest runs fine with these. (also thx to Olivier)

With @fheimes's help, I was able to run autopkgtest successfully.
We figured that libbio-samtools-perl requires a rebuild since it statically links against libbam-dev.

The autopkgtest suite runs like a charm after a rebuild.

Also, submitting the right .debdiff for samtools-legacy with Frank's permission. The original .debdiff does not apply on a clean source tree.

Thanks!

It's a similar situation with the zlib (1:1.2.11.dfsg-2ubuntu1.4)) proposed-migration in focal:
https://people.canonical.com/~ubuntu-archive/proposed-migration/focal/update_excuses.html#zlib

Again focal's version of the samtools-legacy package needed the fix 'PR #1258'.
And based on that, libbio-samtools-perl requires a rebuild since it statically links against libbam-dev.

See PPA: https://launchpad.net/~fheimes/+archive/ubuntu/lp1983255

debdiffs below ...

Subscribing ubuntu-sponsors for sponsoring the SRU for focal....

Thanks Frank and Olivier for the investigations and debdiff.

LGTM. I've uploaded your patch into Kinetic.
I did fix the "Origin: ..." patch header, as it contained a broken URL. Also, I added another "Bug-Ubuntu: ..." header, to reference this bug report, too.

Lastly, I think this patch is worth upstreaming to Debian, could you please use "submittodebian" to send it their way, so we can hopefully get the package back in sync soon? Thanks!

Adding no-change rebuild .debdiff for libbio-samtools-perl (kinetic). To be uploaded once samtools-legacy has finished building. Thanks!

I adopted the version string of the kinetic debdiff and uploaded it into Jammy, which contains the same version of samtools-legacy.

Uploaded the Focal debdiff as well, after applying the same fixes (patch header cleanup) as mentioned in the #11 above.

This bug was fixed in the package samtools-legacy - 0.1.19+dfsg-5ubuntu1

---------------
samtools-legacy (0.1.19+dfsg-5ubuntu1) kinetic; urgency=medium

  * Add backport of upstream commit 515f6df as
    d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch
    in support of fixing 'zlib: compressBound() returns an incorrect result
    on z15'. (LP: #1983255)

 -- Frank Heimes <email address hidden> Mon, 01 Aug 2022 19:03:43 +0200

This bug was fixed in the package libbio-samtools-perl - 1.43-3build4

---------------
libbio-samtools-perl (1.43-3build4) kinetic; urgency=medium

  * No-change rebuild against samtools-legacy (LP: #1983255)

 -- Olivier Gayot <email address hidden> Fri, 12 Aug 2022 11:33:17 +0200

Hello Frank, or anyone else affected,

Accepted samtools-legacy into jammy-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/samtools-legacy/0.1.19+dfsg-5ubuntu0.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-jammy to verification-done-jammy. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-jammy. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

Hello Frank, or anyone else affected,

Accepted samtools-legacy into focal-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/samtools-legacy/0.1.19-4ubuntu0.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-focal to verification-done-focal. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-focal. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

Tested 'samtools-legacy' with the help of a (no-change) rebuild on jammy 'libbio-samtools-perl_1.43-3build3' that makes use of 'libbam-dev_0.1.19+dfsg-5ubuntu0.1' (taken from proposed), which is the binary package of 'samtools-legacy'.
(Notice that 'libbio-samtools-perl' is the package tha is causing the zlib proposed migration regression.)

$ autopkgtest-build-lxd images:ubuntu/jammy/s390x
Using http://squid.internal:3128 as container proxy
Creating autopkgtest-...
$

$ autopkgtest --no-built-binaries --apt-pocket=proposed --apt-upgrade --shell-fail --setup-commands="apt -y -q install software-properties-common; add-apt-repository -y 'deb http://us.ports.ubuntu.com/ubuntu-ports/ jammy-proposed main universe'; apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 73E9E91F16C43C45C621AE3EDF0A28DEFAFEB468; add-apt-repository -y ppa:fheimes/libbio-samtools-perl; apt -y update; apt install -y libbam-dev=0.1.19+dfsg-5ubuntu0.1; apt install -y libbio-samtools-perl=1.43-3build3" libbio-samtools-perl_1.43-3build3.dsc -- lxd autopkgtest/ubuntu/jammy/s390x
...
All tests successful.
Files=1, Tests=4, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.38 cusr 0.07 csys = 0.47 CPU)
Result: PASS
autopkgtest [13:43:04]: test autodep8-perl-recommends: -----------------------]
autopkgtest [13:43:05]: test autodep8-perl-recommends: - - - - - - - - - - results - - - - - - - - - -
autodep8-perl-recommends PASS (superficial)
autopkgtest [13:43:05]: @@@@@@@@@@@@@@@@@@@@ summary
autodep8-perl-build-deps PASS
autodep8-perl PASS (superficial)
autodep8-perl-recommends PASS (superficial)
$

Hence updating tags accordingly to verification-done-jammy.

Tested 'samtools-legacy' with the help of a (no-change) rebuild 'libbio-samtools-perl-1.43-2build2.dsc' on focal that makes use of 'libbam-dev_0.1.19-4ubuntu0.1' (taken from proposed), which is the binary package of 'samtools-legacy'.
(Notice that 'libbio-samtools-perl' is the package tha is causing the zlib proposed migration regression.)

$ autopkgtest-build-lxd images:ubuntu/focal/s390x
Using http://squid.internal:3128 as container proxy
Creating autopkgtest-prepare-...
$

$ autopkgtest --no-built-binaries --apt-pocket=proposed --apt-upgrade --shell-fail --setup-commands="apt -y -q install software-properties-common; add-apt-repository -y 'deb http://us.ports.ubuntu.com/ubuntu-ports/ focal-proposed main universe'; apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 73E9E91F16C43C45C621AE3EDF0A28DEFAFEB468; add-apt-repository -y ppa:fheimes/libbio-samtools-perl; apt -y update; apt install -y libbam-dev=0.1.19-4ubuntu0.1; apt install -y libbio-samtools-perl=1.43-2build2" libbio-samtools-perl_1.43-2build2.dsc -- lxd autopkgtest/ubuntu/focal/s390x
...
All tests successful.
Files=1, Tests=4, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.39 cusr 0.07 csys = 0.48 CPU)
Result: PASS
autopkgtest [15:43:37]: test autodep8-perl-recommends: -----------------------]
autopkgtest [15:43:38]: test autodep8-perl-recommends: - - - - - - - - - - results - - - - - - - - - -
autodep8-perl-recommends PASS (superficial)
autopkgtest [15:43:38]: @@@@@@@@@@@@@@@@@@@@ summary
autodep8-perl-build-deps PASS
autodep8-perl PASS (superficial)
autodep8-perl-recommends PASS (superficial)
$

Hence updating tags accordingly to verification-done-focal.

Adding no-change rebuild debdiff for libbio-samtools-perl (focal).
To be uploaded once samtools-legacy (focal) is done.

Adding no-change rebuild debdiff for libbio-samtools-perl (jammy).
To be uploaded once samtools-legacy (jammy) is done.

I fixed the version number -3build3 => -3build2.1 for Jammy, as the -3build3 version string already exists in the archive. I've added a bug reference to this bug into the changelog, too.

Uploaded into Jammy (unapproved queue).

Version number -2build2 is still fine for Focal, as that is smaller than what we have in Jammy (-3build2). But I've added a bug reference to this bug into the changelog.

Uploaded into Focal (unapproved queue).

Hello Frank, or anyone else affected,

Accepted libbio-samtools-perl into focal-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/libbio-samtools-perl/1.43-2build2 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-focal to verification-done-focal. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-focal. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

Hello Frank, or anyone else affected,

Accepted libbio-samtools-perl into jammy-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/libbio-samtools-perl/1.43-3build2.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-jammy to verification-done-jammy. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-jammy. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

successfully verified on jammy based on libbio-samtools-perl test that uses libbam-dev from samtools legacy (updating tag accordingly)

This bug was fixed in the package samtools-legacy - 0.1.19+dfsg-5ubuntu0.1

---------------
samtools-legacy (0.1.19+dfsg-5ubuntu0.1) jammy; urgency=medium

  * Add backport of upstream commit 515f6df as
    d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch
    in support of fixing 'zlib: compressBound() returns an incorrect result
    on z15'. (LP: #1983255)

 -- Frank Heimes <email address hidden> Mon, 01 Aug 2022 19:03:43 +0200

This bug was fixed in the package libbio-samtools-perl - 1.43-3build2.1

---------------
libbio-samtools-perl (1.43-3build2.1) jammy; urgency=medium

  * No-change rebuild for the samtools-legacy/libbam-dev update. (LP: #1983255)

 -- Frank Heimes <email address hidden> Sat, 20 Aug 2022 13:38:25 +0200

The verification of the Stable Release Update for samtools-legacy has completed successfully and the package is now being released to -updates. Subsequently, the Ubuntu Stable Release Updates Team is being unsubscribed and will not receive messages about this bug report. In the event that you encounter a regression using the package from -updates please report a new bug using ubuntu-bug and tag the bug report regression-update so we can easily find any regressions.

I now also successfully re-did the verification on focal,
hence updating the verification tag accordingly.

This bug was fixed in the package samtools-legacy - 0.1.19-4ubuntu0.1

---------------
samtools-legacy (0.1.19-4ubuntu0.1) focal; urgency=medium

  * Add backport of upstream commit 515f6df as
    d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch
    in support of fixing 'zlib: compressBound() returns an incorrect result
    on z15'. (LP: #1983255)

 -- Frank Heimes <email address hidden> Mon, 08 Aug 2022 13:28:37 +0200

This bug was fixed in the package libbio-samtools-perl - 1.43-2build2

---------------
libbio-samtools-perl (1.43-2build2) focal; urgency=medium

  * No-change rebuild for the samtools-legacy/libbam-dev update. (LP: #1983255)

 -- Frank Heimes <email address hidden> Sat, 20 Aug 2022 16:15:00 +0200