Discussion:
Bug#933828: ncbi-tools6/6.1.20170106+dfsg1-0+deb{9,10}u1
(too old to reply)
Aaron M. Ucko
2019-08-04 03:40:02 UTC
Permalink
Package: release.debian.org
Severity: normal
Tags: stretch buster
User: ***@packages.debian.org
Usertags: pu

Thorsten Alteholz from the FTP Master team recently pointed out a
couple of long-standing copyright-related issues with ncbi-tools6:
some data files turned out to contain non-free portions, and
debian/copyright didn't mention some third-party code I'd previously
overlooked. I've addressed these issues in unstable with ncbi-tools6
6.1.20170106+dfsg1-1.

Thorsten asked me to upload fixes to (old)stable as well, so I've
drafted uploads targeting both releases per
https://salsa.debian.org/med-team/ncbi-tools6/tree/stretch
https://salsa.debian.org/med-team/ncbi-tools6/tree/buster
and the attached debdiffs.

NB: I left stretch at source format 1.0 for now to keep changes to a
minimum, which means it will need an .orig.tar.gz rather than the
identically numbered .orig.tar.xz we have in unstable. If that
discrepancy is a problem, I can cherry-pick more changes; please let
me know.

Could you please take a look?

Thanks!
Aaron M. Ucko
2019-08-09 13:30:01 UTC
Permalink
Post by Aaron M. Ucko
some data files turned out to contain non-free portions
Oops, looks like I'll need to update the autopkgtest in buster (and
unstable) to account for removing these files; I should be able to take
care of it over the weekend.

Sorry for not catching that earlier!
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?***@monk.mit.edu
Adam D. Barratt
2019-08-09 14:30:02 UTC
Permalink
Post by Aaron M. Ucko
Post by Aaron M. Ucko
some data files turned out to contain non-free portions
Oops, looks like I'll need to update the autopkgtest in buster (and
unstable) to account for removing these files; I should be able to take
care of it over the weekend.
Sorry for not catching that earlier!
As a side note, having just spotted the subject header - if you're
looking at updating the package in both stretch and buster then that
needs two distinct tracking bugs, please. They're distinct uploads that
go through different queues and may be released (or not) at different
times.

Regards,

Adam
Aaron M. Ucko
2019-08-09 14:40:01 UTC
Permalink
bts clone 933828 -1
bts tags 933828 - buster
bts retitle 933828 ncbi-tools6/6.1.20170106+dfsg1-0+deb9u1
bts tags -1 - stretch
bts retitle -1 ncbi-tools6/6.1.20170106+dfsg1-0+deb10u1
thanks
Post by Adam D. Barratt
As a side note, having just spotted the subject header - if you're
looking at updating the package in both stretch and buster then that
needs two distinct tracking bugs, please. They're distinct uploads
that go through different queues and may be released (or not) at
different times.
Got it, thanks; cloning and tuning accordingly. On a somewhat related
note, should I cite the tracking bugs in my changelogs?
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?***@monk.mit.edu
Aaron M. Ucko
2019-08-09 14:50:02 UTC
Permalink
clone 933828 -1
tags 933828 - buster
retitle 933828 ncbi-tools6/6.1.20170106+dfsg1-0+deb9u1
tags -1 - stretch
retitle -1 ncbi-tools6/6.1.20170106+dfsg1-0+deb10u1
thanks
Post by Aaron M. Ucko
Got it, thanks; cloning and tuning accordingly.
This time for real. (Long week.)
Post by Aaron M. Ucko
On a somewhat related note, should I cite the tracking bugs in my
changelogs?
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?***@monk.mit.edu
Adam D. Barratt
2019-08-10 11:40:01 UTC
Permalink
On Fri, 2019-08-09 at 10:37 -0400, Aaron M. Ucko wrote:
[...]
Post by Adam D. Barratt
As a side note, having just spotted the subject header - if you're
looking at updating the package in both stretch and buster then that
needs two distinct tracking bugs, please. They're distinct uploads
that go through different queues and may be released (or not) at
different times.
Got it, thanks; cloning and tuning accordingly.  On a somewhat
related note, should I cite the tracking bugs in my changelogs?
No. You could mention them in passing if you would like, but there's
certainly no requirement to - users tend to care about the actual
fixes, not the process.

In any case, please *do not* close the release.d.o bugs in your
uploads. That will happen (via us) once the upload has actually made it
to {,old}stable in a point release.

Regards,

Adam
Aaron M. Ucko
2019-08-12 02:50:02 UTC
Permalink
[Switching to Buster version of this request, which got the new number.]
Post by Adam D. Barratt
No. You could mention them in passing if you would like, but there's
certainly no requirement to - users tend to care about the actual
fixes, not the process.
Got it, thanks, just checking.
Post by Adam D. Barratt
In any case, please *do not* close the release.d.o bugs in your
uploads. That will happen (via us) once the upload has actually made it
to {,old}stable in a point release.
Don't worry, I would have at most added a "(See: #93xxxx)" somewhere.

At any rate, I've just uploaded 6.1.20170106+dfsg1-2 to unstable with
the autopkgtest regression fix, and folded that fix into my proposed
6.1.20170106+dfsg1-0+deb10u1 stable update, which now has the attached
debdiff. (I've also pushed these changes to my buster branch on salsa.)
Sorry for the debian/patches/debian-changes diff noise, which is an
artifact of my dgit usage style.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?***@monk.mit.edu
Adam D. Barratt
2019-08-13 17:30:02 UTC
Permalink
Control: tags -1 + confirmed
Post by Aaron M. Ucko
[Switching to Buster version of this request, which got the new number.]
[...]
Post by Aaron M. Ucko
At any rate, I've just uploaded 6.1.20170106+dfsg1-2 to unstable with
the autopkgtest regression fix, and folded that fix into my proposed
6.1.20170106+dfsg1-0+deb10u1 stable update, which now has the
attached
debdiff.  (I've also pushed these changes to my buster branch on
salsa.)
Please go ahead; thanks.

Regards,

Adam
Aaron M. Ucko
2019-08-14 01:40:01 UTC
Permalink
Post by Adam D. Barratt
Please go ahead; thanks.
Uploaded, 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/?***@monk.mit.edu
Adam D. Barratt
2019-08-20 08:00:01 UTC
Permalink
Post by Aaron M. Ucko
Post by Adam D. Barratt
Please go ahead; thanks.
Uploaded, thanks!
Unfortunately the autopkgtest appears to be failing, presumably related
to the file removal. From
https://ci.debian.net/data/autopkgtest/stable/amd64/n/ncbi-tools6/2756273/log.gz
:

---vecscreen test---
[vecscreen] FATAL ERROR: Database UniVec was not found or does not exist

Regards,

Adam

Adam D. Barratt
2019-08-13 17:30:01 UTC
Permalink
Control: tags -1 + confirmed
Post by Aaron M. Ucko
Thorsten Alteholz from the FTP Master team recently pointed out a
some data files turned out to contain non-free portions, and
debian/copyright didn't mention some third-party code I'd previously
overlooked.  I've addressed these issues in unstable with ncbi-tools6
6.1.20170106+dfsg1-1.
Thorsten asked me to upload fixes to (old)stable as well, so I've
drafted uploads targeting both releases per
https://salsa.debian.org/med-team/ncbi-tools6/tree/stretch
https://salsa.debian.org/med-team/ncbi-tools6/tree/buster
and the attached debdiffs.
NB: I left stretch at source format 1.0 for now to keep changes to a
minimum, which means it will need an .orig.tar.gz rather than the
identically numbered .orig.tar.xz we have in unstable.  If that
discrepancy is a problem, I can cherry-pick more changes; please let
me know.
I think it ends up being OK, but let's see. :-)

Please go ahead with the stretch upload.

Regards,

Adam
Aaron M. Ucko
2019-08-14 01:40:02 UTC
Permalink
Post by Adam D. Barratt
Please go ahead with the stretch upload.
Uploaded, 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/?***@monk.mit.edu
Adam D Barratt
2019-08-16 21:00:01 UTC
Permalink
package release.debian.org
tags 933828 = stretch pending
thanks

Hi,

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

Thanks for your contribution!

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

Package: ncbi-tools6
Version: 6.1.20170106+dfsg1-0+deb9u1

Explanation: repackage without non-free data/UniVec.*
Adam D Barratt
2019-08-16 21:00:01 UTC
Permalink
package release.debian.org
tags 934311 = buster pending
thanks

Hi,

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

Thanks for your contribution!

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

Package: ncbi-tools6
Version: 6.1.20170106+dfsg1-0+deb10u1

Explanation: repackage without non-free data/UniVec.*
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