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Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

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  Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 "Aaron M. Ucko" <ucko@debian.org> - 2023-07-13 05:00 +0200
    Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 "Adam D. Barratt" <adam@adam-barratt.org.uk> - 2023-07-13 20:00 +0200
      Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 ucko@debian.org (Aaron M. Ucko) - 2023-07-13 20:20 +0200
        Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 ucko@debian.org (Aaron M. Ucko) - 2023-07-14 05:30 +0200
          Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 "Adam D. Barratt" <adam@adam-barratt.org.uk> - 2023-07-14 18:00 +0200
            Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 ucko@debian.org (Aaron M. Ucko) - 2023-07-14 21:20 +0200
              Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1 "Adam D. Barratt" <adam@adam-barratt.org.uk> - 2023-07-14 21:30 +0200
    Bug#1040953: sra-sdk 3.0.3+dfsg-6~deb12u1 flagged for acceptance Adam D Barratt <adam@adam-barratt.org.uk> - 2023-07-15 14:40 +0200

#1153980 — Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

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Package: release.debian.org
Severity: normal
Tags: bookworm
User: release.debian.org@packages.debian.org
Usertags: pu
X-Debbugs-Cc: sra-sdk@packages.debian.org
Control: affects -1 + src:sra-sdk

[ Reason ]
Per #1039621, the new libngs-jni package accidentally wound up with
bad content (unexpanded variables in the key symlink's source *and*
target) that rendered it useless.

[ Impact ]
This package's reverse dependencies, from libngs-java on up, will be
broken unless libncbi-ngs-dev happens to be installed.

[ Tests ]
Various affected packages have autopkgtests, but they evidently missed
the relevant bug, having presumably wound up running with
libncbi-ngs-dev additionally installed.  (The tests did catch the
need for architecture restrictions that made it into bookworm, FWIW.)

[ Risks ]
Minimal -- trivial fix, working in testing and unstable with no
further changes from stable.

[ Checklist ]
  [*] *all* changes are documented in the d/changelog
  [v] I reviewed all changes and I approve them
  [v] attach debdiff against the package in (old)stable
  [v] the issue is verified as fixed in unstable

[ Changes ]
Tweak debian/rules to make the necessary substitutions in
libngs-java.links.in.

[ Other info ]
In reviewing the debdiff, I see that one of my teammates pushed a
debian/salsa-ci.yml update without a corresponding changelog note that
consequently slipped into -6 undocumented; what should I do about it
at this point?

I've held off on cleaning up a long-dangling symlink in a different
binary package (sra-toolkit, #1040391) but can readily throw that in
if you'd like.

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#1154068

Control: tags -1 + confirmed

On Wed, 2023-07-12 at 22:37 -0400, Aaron M. Ucko wrote:
> Per #1039621, the new libngs-jni package accidentally wound up with
> bad content (unexpanded variables in the key symlink's source *and*
> target) that rendered it useless.

+sra-sdk (3.0.3+dfsg-6~deb12u1) bookworm; urgency=medium
+
+  * Reupload to bookworm (stable).  (Closes: #10nnnnn).

If you were intending to close this p-u request there, please don't.
The bug will get closed once the updated package is in stable as part
of a point release.

--- sra-sdk-3.0.3+dfsg/debian/.gitignore	2023-02-24 05:52:27.000000000 -0500
+++ sra-sdk-3.0.3+dfsg/debian/.gitignore	1969-12-31 19:00:00.000000000 -0500
@@ -1,16 +0,0 @@

Is the removal of .gitignore intentional?

The fix itself looks fine, so please feel free to go ahead (with the
Closes: removed and possibly with .gitignore restored if appropriate).

Regards,

Adam

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#1154074

"Adam D. Barratt" <adam@adam-barratt.org.uk> writes:

> If you were intending to close this p-u request there, please don't.
> The bug will get closed once the updated package is in stable as part
> of a point release.

Ah, right, I'll leave that off, then.

> Is the removal of .gitignore intentional?

No, that was an artifact of using an atypical build procedure; sorry for
the noise.  (I'd held off on committing these tentative changes, so gbp
would have required a special flag; I substituted plain debuild but
evidently didn't get its flags quite right.)

> The fix itself looks fine, so please feel free to go ahead (with the
> Closes: removed and possibly with .gitignore restored if appropriate).

Will do, thanks!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

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#1154131

ucko@debian.org (Aaron M. Ucko) writes:

>> The fix itself looks fine, so please feel free to go ahead (with the
>> Closes: removed and possibly with .gitignore restored if appropriate).
>
> Will do, thanks!

Uploaded, final debdiff confirmed not to touch .gitignore.  Thanks!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

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#1154202

On Thu, 2023-07-13 at 23:21 -0400, Aaron M. Ucko wrote:
> ucko@debian.org (Aaron M. Ucko) writes:
> 
> > > The fix itself looks fine, so please feel free to go ahead (with
> > > the
> > > Closes: removed and possibly with .gitignore restored if
> > > appropriate).
> > 
> > Will do, thanks!
> 
> Uploaded, final debdiff confirmed not to touch .gitignore.  Thanks!
> 

FWIW the auto-generated debdiff disagrees - 
https://release.debian.org/proposed-updates/bookworm_diffs/sra-sdk_3.0.3+dfsg-6~deb12u1.debdiff

 .gitignore   |   16 ----------------

Assuming that you would prefer not to include that change, it's up to
you whether you'd prefer to upload ~deb12u2 as an additional revision
that simply re-adds the file, or we can reject the current package and
you can re-upload as ~deb12u1 again.

Regards,

Adam

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#1154243

"Adam D. Barratt" <adam@adam-barratt.org.uk> writes:

> FWIW the auto-generated debdiff disagrees - 
> https://release.debian.org/proposed-updates/bookworm_diffs/sra-sdk_3.0.3+dfsg-6~deb12u1.debdiff

Please clear the path for another 3.0.3+dfsg-6~deb12u1 upload, thanks.

Sorry about that -- I'd compared against my -6 because that was handier
on the relevant host, but my so-far customary workflow turned out to
have yielded the same exclusion.  I found a reasonably clean way of
dropping the exclusion without needing a new tag: manually running

  dpkg-source -b . -Inonexistent

I will look into adjusting my workflow to DTRT.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu

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#1154247

On Fri, 2023-07-14 at 15:09 -0400, Aaron M. Ucko wrote:
> "Adam D. Barratt" <adam@adam-barratt.org.uk> writes:
> 
> > FWIW the auto-generated debdiff disagrees - 
> > https://release.debian.org/proposed-updates/bookworm_diffs/sra-sdk_3.0.3+dfsg-6~deb12u1.debdiff
> 
> Please clear the path for another 3.0.3+dfsg-6~deb12u1 upload,
> thanks.
> 

Thanks for the quick follow-up.

I've flagged the current upload for rejection. Feel free to re-upload
once that gets actioned.

Regards,

Adam

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#1154365 — Bug#1040953: sra-sdk 3.0.3+dfsg-6~deb12u1 flagged for acceptance

package release.debian.org
tags 1040953 = bookworm pending
thanks

Hi,

The upload referenced by this bug report has been flagged for acceptance into the proposed-updates queue for Debian bookworm.

Thanks for your contribution!

Upload details
==============

Package: sra-sdk
Version: 3.0.3+dfsg-6~deb12u1

Explanation: fix installation of files in libngs-java

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