Your message dated Sat, 27 May 2023 11:33:06 +0200
with message-id
<CAM8zJQttPX5R3vOzwJs29SDFaZ9uAXcsXdG1p=tp+oh-udv...@mail.gmail.com>
and subject line Re: [Debian-med-packaging] Bug#1036761: unblock:
kleborate/2.3.1-2
has caused the Debian Bug report #1036761,
regarding unblock: kleborate/2.3.1-2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
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--
1036761: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1036761
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
User: release.debian....@packages.debian.org
Usertags: unblock
X-Debbugs-Cc: klebor...@packages.debian.org
Control: affects -1 + src:kleborate
Please unblock package kleborate
[ Reason ]
kleborate is affected by the release critical upgrade bug
#1036743 identified by Andreas Beckmann (Thanks for QA tests!).
[ Impact ]
If the unblock is not granted, the package may have inconsistent
blast databases when ncbi-blast+ is upgraded after kleborate.
[ Tests ]
I ran manually the upgrade paths described in #1036743, comment
#30, to make sure the initial issue was reproducible somehow and
actually fixed by the changes. For extra safety, I also ran a
few more basic piuparts runs since some prerm modification was
involved.
I would have hoped to point to Salsa CI results, but they have a
long standing issues at their build steps. Other automated
tests were the build time checks and an autopkgtest manually run
on amd64.
Autobuilders look to have managed to get kleborate to build
anywhere where its build dependencies are already available.
Debci autopkgtests are pending; I don't expect difficulties on
this front as changes would have little risk to break in an
architecture specific way anyway.
[ Risks ]
Little risks are identified: changes involve a change in
maintainer script but they should be covered by the piuparts
tests already done, otherwise this is a leaf package so the area
of effect of any mishap should be limited to the package.
[ Checklist ]
[*] all changes are documented in the d/changelog
[*] I reviewed all changes and I approve them
[*] attach debdiff against the package in testing
[ Other info ]
Thanks for your work on putting together the bookworm release!
unblock kleborate/2.3.1-2
Have a nice day, :)
Étienne.
diff -Nru kleborate-2.3.1/debian/changelog kleborate-2.3.1/debian/changelog
--- kleborate-2.3.1/debian/changelog 2023-02-06 07:37:51.000000000 +0100
+++ kleborate-2.3.1/debian/changelog 2023-05-25 14:48:18.000000000 +0200
@@ -1,3 +1,18 @@
+kleborate (2.3.1-2) unstable; urgency=medium
+
+ * d/{rules,*.prerm}: cleanup .fasta.{ndb,ntf} files
+ kleborate binary package used to embed autogenerated files depending
+ on makeblastdb version at both build time and postinst time. When
+ there is a discrepancy of makeblastdb version between the package
+ build and the package installation, for instance during a major
+ operating system upgrade, there can be a mismatch of int the
+ .fasta.ndb and .fasta.ntf files produced and expected. This change
+ gets rid of the build time artifacts to solely rely on the
+ post-installation artifacts, which will be more consistent and won't
+ break the package consistency. (Closes: #1036743)
+
+ -- Étienne Mollier <emoll...@debian.org> Thu, 25 May 2023 14:48:18 +0200
+
kleborate (2.3.1-1) unstable; urgency=medium
* New upstream version
diff -Nru kleborate-2.3.1/debian/kleborate.prerm
kleborate-2.3.1/debian/kleborate.prerm
--- kleborate-2.3.1/debian/kleborate.prerm 2023-02-06 07:37:51.000000000
+0100
+++ kleborate-2.3.1/debian/kleborate.prerm 2023-05-25 14:48:18.000000000
+0200
@@ -5,6 +5,8 @@
case "$1" in
remove|purge|upgrade|deconfigure)
rm -f /usr/lib/python3/dist-packages/kleborate/data/*.fasta.nin
+ rm -f /usr/lib/python3/dist-packages/kleborate/data/*.fasta.ndb
+ rm -f /usr/lib/python3/dist-packages/kleborate/data/*.fasta.ntf
;;
failed-upgrade)
;;
diff -Nru kleborate-2.3.1/debian/rules kleborate-2.3.1/debian/rules
--- kleborate-2.3.1/debian/rules 2023-02-06 07:37:51.000000000 +0100
+++ kleborate-2.3.1/debian/rules 2023-05-25 14:48:18.000000000 +0200
@@ -7,8 +7,14 @@
override_dh_install:
dh_install
- # fasta.nin files will be (re)build at package installation time to not
contain build path
+ # fasta.nin files will be (re)build at package installation time to not
+ # contain build path. Other fasta.* are rebuilt by makeblastdb and may
+ # cause inconsistencies in the package itself when makeblastdb is
+ # upgraded and changes format, e.g. during a major operating system
+ # upgrade. See Bug#1036743.
find debian -name "*.fasta.nin" -delete
+ find debian -name "*.fasta.ndb" -delete
+ find debian -name "*.fasta.ntf" -delete
override_dh_fixperms:
dh_fixperms
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
On Thu, 25 May 2023 at 16:21, Étienne Mollier <emoll...@debian.org> wrote:
> unblock kleborate/2.3.1-2
Unblocked, thanks.
--- End Message ---
