Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-22 Thread Andreas Tille
Am Sun, May 22, 2022 at 07:43:35PM +0530 schrieb Nilesh Patra:
> >I've just commited a patch thet ignores the not yet packaged test
> >dependency which causes the test failure.  In any case r-bioc-scater
> 
> Then please make an upload.

https://salsa.debian.org/r-pkg-team/r-bioc-scater/-/jobs/2796964

   ->>   builddeps:. : Depends: r-cran-rcppml but it is not installable
 E: Unable to correct problems, you have held broken packages.

There was no other patch than the one I created ... and I think it
makes sense to wait for Build-Depends clearing new.  Thus I've set
a "block by".

> >needs to wait for r-cran-rcppml in new - may be some removal from
> >testing is needed in any case.
> 
> No, not really. I had already edited the description file in the last upload 
> to unbreak the transition, although I didn't observe the failing test locally.

Are you sure you pushed?

Kind regards

Andreas.

> >> [1] https://tracker.debian.org/pkg/r-bioc-scater
> >> [2] https://ci.debian.net/packages/r/r-bioc-scater/testing/amd64/
 

-- 
http://fam-tille.de



Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-22 Thread Nilesh Patra



On 22 May 2022 7:05:18 pm IST, Andreas Tille  wrote:
>Hi Graham,
>
>Am Sun, May 22, 2022 at 09:09:01AM +0200 schrieb Graham Inggs:
>> It looks like the only blocker now is waiting for r-bioc-scater [1] to age:
>> 
>> Too young, only 2 of 5 days old
>> 
>> It doesn't get 2-day migration because its autopkgtest regressed in
>> testing, sometime around 2021-09-23 [2].
>
>I've just commited a patch thet ignores the not yet packaged test
>dependency which causes the test failure.  In any case r-bioc-scater

Then please make an upload.

>needs to wait for r-cran-rcppml in new - may be some removal from
>testing is needed in any case.

No, not really. I had already edited the description file in the last upload to 
unbreak the transition, although I didn't observe the failing test locally.

>> [1] https://tracker.debian.org/pkg/r-bioc-scater
>> [2] https://ci.debian.net/packages/r/r-bioc-scater/testing/amd64/
>

-- 
Regards,
Nilesh



Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-22 Thread Andreas Tille
Hi Graham,

Am Sun, May 22, 2022 at 09:09:01AM +0200 schrieb Graham Inggs:
> It looks like the only blocker now is waiting for r-bioc-scater [1] to age:
> 
> Too young, only 2 of 5 days old
> 
> It doesn't get 2-day migration because its autopkgtest regressed in
> testing, sometime around 2021-09-23 [2].

I've just commited a patch thet ignores the not yet packaged test
dependency which causes the test failure.  In any case r-bioc-scater
needs to wait for r-cran-rcppml in new - may be some removal from
testing is needed in any case.
 
> I'll file a separate bug for that.

Feel free to do so but for the moment the issue is fixed in Git and
will be uploaded once the new Build-Depends is available.

Kind regards

  Andreas.
 
> [1] https://tracker.debian.org/pkg/r-bioc-scater
> [2] https://ci.debian.net/packages/r/r-bioc-scater/testing/amd64/

-- 
http://fam-tille.de



Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-22 Thread Graham Inggs
Hi Nilesh

It looks like the only blocker now is waiting for r-bioc-scater [1] to age:

Too young, only 2 of 5 days old

It doesn't get 2-day migration because its autopkgtest regressed in
testing, sometime around 2021-09-23 [2].

I'll file a separate bug for that.

Regards
Graham


[1] https://tracker.debian.org/pkg/r-bioc-scater
[2] https://ci.debian.net/packages/r/r-bioc-scater/testing/amd64/



Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-21 Thread Graham Inggs
Hi Nilesh

On Sat, 21 May 2022 at 07:03, Nilesh Patra  wrote:

It looks like britney has already figured these out:

> r-bioc-annotationdbiset ignore for r-bioc-annotationhub (version in 
> unstable passes)
> r-bioc-scran/beachmat   Please run tests with new version of biocparallel

I'll wait a bit to see if these get resolved once r-bioc-bluster is a candidate:

> r-bioc-biocneighborsset r-bioc-bluster to ignore (version in unstable 
> passes)
> r-bioc-biocparallel set r-bioc-bluster to ignore (version 
> in unstable passes)

Regards
Graham



Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-20 Thread Nilesh Patra

Hi Graham,

I did some work to cleanup the rest stuff meanwhile, and need
your help to ignore some of the CI temporarily to complete the migration; and
also because unstable counterparts pass.

I have pasted a list at the end of this email, please see to it.

--
Best,
Nilesh



Package Reverse dependency

r-bioc-annotationdbiset ignore for r-bioc-annotationhub (version in 
unstable passes)
r-bioc-scran/beachmat   Please run tests with new version of biocparallel
r-bioc-biocneighborsset r-bioc-bluster to ignore (version in unstable 
passes)
r-bioc-biocparallel set r-bioc-bluster to ignore (version 
in unstable passes)



Other caveats:
r-bioc-singler/r-bioc-scran (at the time of writing this email) need to run 
with new version
of biocparallel in unstable
and the versions of reverse-deps should point to its unstable version



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Bug#1010422: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Andreas Tille
Hi Paul,

Am Thu, May 19, 2022 at 01:07:59PM +0200 schrieb Paul Gevers:
> @tille, removals are work for *us*, they are not free lunch. Please fix the
> package that prevent migration.

There is no clean fix.  The packages featuring r-bioc-api-3.15 just need
some new predependencies.  These are hanging in new since some days.
Just pretending the new predependencies are not needed is not a fix,
IMHO.  So we can do nothing but wait.
 
> PS: for every transition we ask packages that need to go through NEW to be
> prepared in experimental such that during the transition, we don't need to
> wait for it.

I agree that in principle experimental would be cleaner.  On the other
hand its a lot more manual work.  I wonder whether it is a real problem
to leave the new r-bioc-* packages waiting in unstable until the
preconditions might have cleared NEW.  Is this not yet finished
transition in some way creating work?  I mean we have uploaded lots of
packages pretty fast - hopefully faster than in other transitions.  So
we are now waiting a bit.  May be my view on transitions is to naive and
there is really a problem if its delayed a couple of days more.  I plan
to give some hint to ftpmaster in the beginning of next week but I do
not want to create more pressure than needed.

Kind regards

 Andreas.

-- 
http://fam-tille.de



Bug#1010422: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Nilesh Patra



On 19 May 2022 2:25:23 pm IST, Andreas Tille  wrote:
>Am Thu, May 19, 2022 at 01:41:12PM +0530 schrieb Nilesh Patra:
>> 
>> I think we can workaround these anyway by editing the DESCRIPTION file -- 
>> maybe I'll do so and upload either late in the night today or early morning 
>> Tom.
>
>I do not think that editing DESCRIPTION is the prefered way to
>fix our transition.  As I wrote in my other mail removing them
>from testing manually should do the trick as well, IMHO.

I disagree.

I don't really think stalling the migration just for a couple of packages is a 
sensible thing to do.

There is not a functional difference (real API change) so keeping a couple of 
packages outdated (and that too because pre-deps are in new) is no big deal.

We already have tons of cran stuff being backdated due to several reasons, I 
don't think this situation is very different. I know the bioc api is different 
but there's no functional difference in working of package at all.

I would rather do what it takes and complete the transition, so as to unbreak 
packages and also not consume un-necessary bandwidth of release team members.

And so, I'd continue to patch description and upload anyway. If you're 
very/extremely against it, please do let me know soon so we figure out 
something else.

--
Best,
Nilesh



Bug#1010422: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Paul Gevers

Hi,

On 19-05-2022 10:55, Andreas Tille wrote:

Am Thu, May 19, 2022 at 01:41:12PM +0530 schrieb Nilesh Patra:

I think we can workaround these anyway by editing the DESCRIPTION file -- maybe 
I'll do so and upload either late in the night today or early morning Tom.


I do not think that editing DESCRIPTION is the prefered way to
fix our transition.  As I wrote in my other mail removing them
from testing manually should do the trick as well, IMHO.


Well, I just learned that some/most of these "required" uploads in this 
transition are not needed because of incompatibility of the package with 
the new api, but just your tooling being broken (in my opinion). If 
packages requiring r-api-bioc-* work with the next version, they should 
just pick up the r-api-bioc-* version when they are rebuild, like we do 
with nearly all other ecosystem in Debian. Only packages that don't work 
need an upload.


If all it takes is this;
https://salsa.debian.org/r-pkg-team/r-bioc-mofa/-/blob/7b010dcd1947e2b8b26da3ab49b957715cb83b5c/debian/patches/bioc-3.15.patch
to get the package working with the fresh bioconducter, that really 
shouldn't need manual changes and should be able to be picked up 
automatically.


@tille, removals are work for *us*, they are not free lunch. Please fix 
the package that prevent migration.


Paul

PS: for every transition we ask packages that need to go through NEW to 
be prepared in experimental such that during the transition, we don't 
need to wait for it.


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Bug#1010422: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Andreas Tille
Am Thu, May 19, 2022 at 09:40:23AM +0200 schrieb Paul Gevers:
> Package: release.debian.org
> User: release.debian@packages.debian.org
> Usertag: britney
> 
> Hi,
> 
> On 11-05-2022 12:34, Graham Inggs wrote:
> > Yes, please go ahead.
> > 
> > Tracker is at:
> > https://release.debian.org/transitions/html/r-api-bioc-3.15.html
> 
> There's three package still waiting for an upload, r-bioc-progeny,
> r-bioc-monocle and r-bioc-scater. When is the ETA for those?

Once their new (Build-)Depends

r-cran-leidenbase
r-cran-rcppml
r-bioc-metapod

will have cleared new.  Since this is really hard to predict it might
possibly help to remove the said packages from testing meanwhile.
 
Kind regards

  Andreas.

-- 
http://fam-tille.de



Bug#1010422: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Andreas Tille
Hi Nilesh,

Am Thu, May 19, 2022 at 01:41:12PM +0530 schrieb Nilesh Patra:
> 
> I think we can workaround these anyway by editing the DESCRIPTION file -- 
> maybe I'll do so and upload either late in the night today or early morning 
> Tom.

I do not think that editing DESCRIPTION is the prefered way to
fix our transition.  As I wrote in my other mail removing them
from testing manually should do the trick as well, IMHO.
 
> Thanks Paul for your work!

+1
 
Kind regards

 Andreas. 

-- 
http://fam-tille.de



Bug#1010422: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Nilesh Patra



Hi,

On 19 May 2022 1:10:23 pm IST, Paul Gevers  wrote:
>Package: release.debian.org
>User: release.debian@packages.debian.org
>Usertag: britney
>
>Hi,
>
>On 11-05-2022 12:34, Graham Inggs wrote:
>> Yes, please go ahead.
>> 
>> Tracker is at:
>> https://release.debian.org/transitions/html/r-api-bioc-3.15.html
>
>There's three package still waiting for an upload, r-bioc-progeny, 
>r-bioc-monocle and r-bioc-scater. When is the ETA for those?

They are blocked by packages in NEW so whenever FTP masters accept these.

I think we can workaround these anyway by editing the DESCRIPTION file -- maybe 
I'll do so and upload either late in the night today or early morning Tom.

>Apart from these missing uploads, there's a bunch of autopkgtest regressions 
>blocking the migration of the set [1]. I have a hunch that quite some 
>regressions are caused by missing *versioned* (test) dependencies that cause 
>incompatible sets to be tested.

Many of these are also due to versioned depends I guess.

> Thinking more about it that could very well be a bug in our migration 
> software failing to properly handle the Provides which glues this all 
> together and which is uniquely provided by r-bioc-biocgenerics. Remember that 
> our migration software tries to determine the minimal (source based) [...]

I know, if that could be improved, it'd be awesome otherwise it's a pain to 
deal with. Even for an earlier r-base transition, I had to do bogus uploads to 
make Britney happy.

It does not make much sense to me to add a breaks for things and clutter 
d/control. There's no real usecase to be honest since there's already a version 
dep on r/r-api-bioc respectively.

> if the manual pinning helps, we'll need to see how to improve it.

Thanks Paul for your work!

>[1]
https://people.debian.org/~elbrus/ci/regressions.html
>[2] 
>https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-megadepth/21776746/log.gz


--
Best,
Nilesh



Bug#1010422: Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Graham Inggs
Hi

On Thu, 19 May 2022 at 09:45, Paul Gevers  wrote:
> There's three package still waiting for an upload, r-bioc-progeny,
> r-bioc-monocle and r-bioc-scater. When is the ETA for those?

In addition, there is r-bioc-grohmm which I happened to notice dropped
off the tracker during the transition.
i.e. it lost its dependency on r-api-bioc-3.14, but did not pick up
one on r-api-bioc-3.15.

I do not know if there were any others.

Regards
Graham



Bug#1011265: Britney fails to pin complete set in "Provides" api transitions [Was: Bug#1010422: transition: r-api-bioc-3.15]

2022-05-19 Thread Paul Gevers

Package: release.debian.org
User: release.debian@packages.debian.org
Usertag: britney

Hi,

On 11-05-2022 12:34, Graham Inggs wrote:

Yes, please go ahead.

Tracker is at:
https://release.debian.org/transitions/html/r-api-bioc-3.15.html


There's three package still waiting for an upload, r-bioc-progeny, 
r-bioc-monocle and r-bioc-scater. When is the ETA for those?


Apart from these missing uploads, there's a bunch of autopkgtest 
regressions blocking the migration of the set [1]. I have a hunch that 
quite some regressions are caused by missing *versioned* (test) 
dependencies that cause incompatible sets to be tested. Thinking more 
about it that could very well be a bug in our migration software failing 
to properly handle the Provides which glues this all together and which 
is uniquely provided by r-bioc-biocgenerics. Remember that our migration 
software tries to determine the minimal (source based) set (deducted 
from real package relations, i.e. Depends, Conflicts and Breaks) that 
needs to come from unstable to be tested in testing. You can see which 
source packages it deducted from the third line of each autopkgtest log. 
E.g. [2] has:

--pin-packages=unstable=src:r-bioc-megadepth,src:r-bioc-biocgenerics

And than later:
The following packages have unmet dependencies:
 r-bioc-rtracklayer : Depends: r-api-bioc-3.14
  Depends: r-bioc-rsamtools (>= 1.31.2) but it is 
not going to be installed
  Depends: r-bioc-genomicalignments (>= 1.15.6) but 
it is not going to be installed


I'll see if some manual addition pinning helps, but checking the status 
in unstable may also be a good way to see what the status is. In the 
mean time, this mail is also a bug report against britney, if the manual 
pinning helps, we'll need to see how to improve it.


Paul

[1] https://people.debian.org/~elbrus/ci/regressions.html
[2] 
https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-megadepth/21776746/log.gz


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Bug#1010422: transition: r-api-bioc-3.15

2022-05-11 Thread Graham Inggs
Control: tags -1 = confirmed

Hi Nilesh, Dylan

On Wed, 11 May 2022 at 11:33, Nilesh Patra  wrote:
>
>
>
> On 11 May 2022 2:06:08 pm IST, "Dylan Aïssi"  wrote:
> >Hi all,
> >
> >> Am Fri, May 06, 2022 at 06:10:52PM +0530 schrieb Nilesh Patra:
> >> >
> >> > I have done so, I think we can start the transition. Please consider 
> >> > pushing
> >> > the buttons to get the tracker up :)
> >>
> >
> >To be sure, have we the green light from the release team to start
> >this transition?
>
>
> @Graham, could you let us know? -- Should we start?

Yes, please go ahead.

Tracker is at:
https://release.debian.org/transitions/html/r-api-bioc-3.15.html

Regards
Graham



Bug#1010422: transition: r-api-bioc-3.15

2022-05-11 Thread Nilesh Patra



On 11 May 2022 2:06:08 pm IST, "Dylan Aïssi"  wrote:
>Hi all,
>
>> Am Fri, May 06, 2022 at 06:10:52PM +0530 schrieb Nilesh Patra:
>> >
>> > I have done so, I think we can start the transition. Please consider 
>> > pushing
>> > the buttons to get the tracker up :)
>>
>
>To be sure, have we the green light from the release team to start
>this transition?


@Graham, could you let us know? -- Should we start?

--
Best,
Nilesh



Bug#1010422: transition: r-api-bioc-3.15

2022-05-11 Thread Dylan Aïssi
Hi all,

> Am Fri, May 06, 2022 at 06:10:52PM +0530 schrieb Nilesh Patra:
> >
> > I have done so, I think we can start the transition. Please consider pushing
> > the buttons to get the tracker up :)
>

To be sure, have we the green light from the release team to start
this transition?

Best,
Dylan



Bug#1010422: transition: r-api-bioc-3.15

2022-05-06 Thread Andreas Tille
Hi Nilesh,

Am Fri, May 06, 2022 at 06:10:52PM +0530 schrieb Nilesh Patra:
> 
> I think I did the changes as I wanted to, all graphics packages and all the
> important cran packages for that matter (including rmatrix) have now migrated.

Thanks a lot.
  
> > Please remove the moreinfo tag once you are ready.
> 
> I have done so, I think we can start the transition. Please consider pushing
> the buttons to get the tracker up :)

:-)
 
> PS: I will not be able to contribute in any capacity to bioc transition and 
> hope
> Andreas, you, Dylan et. al. would complete this :)

Same for me this weekend and start of next week.  I'm traveling and have
intentionally just my "traveling" laptop.  So I'm extremely limited with
contributions ... things will last as long they need.

Kind regards

  Andreas.

-- 
http://fam-tille.de



Bug#1010422: transition: r-api-bioc-3.15

2022-05-06 Thread Nilesh Patra
Control: tags -1 - moreinfo

Hi Graham/Andreas,

On Tue, May 03, 2022 at 04:04:22PM +0200, Graham Inggs wrote:
> On Tue, 3 May 2022 at 15:51, Nilesh Patra  wrote:
> > I am now trying to get ggplot2 and friends in testing. Please give
> > it time until this weekend to migrate after which I will remove
> > my hacks and re-upload.
> 
> Please also look at rmatrix, it is a build-dependency of several
> r-bioc-* packages.

I think I did the changes as I wanted to, all graphics packages and all the
important cran packages for that matter (including rmatrix) have now migrated.
 
> > Let's start bioc transition after this is done.
> 
> Please remove the moreinfo tag once you are ready.

I have done so, I think we can start the transition. Please consider pushing
the buttons to get the tracker up :)

PS: I will not be able to contribute in any capacity to bioc transition and hope
Andreas, you, Dylan et. al. would complete this :)

-- 
Best,
Nilesh


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Bug#1010422: transition: r-api-bioc-3.15

2022-05-03 Thread Nilesh Patra
On Tue, May 03, 2022 at 04:04:22PM +0200, Graham Inggs wrote:
> Control: tags -1 + moreinfo
> > I am now trying to get ggplot2 and friends in testing. Please give
> > it time until this weekend to migrate after which I will remove
> > my hacks and re-upload.
> 
> Please also look at rmatrix, it is a build-dependency of several
> r-bioc-* packages.

That'd get in once ggplot2 and friends transition. Should be soonish.

> > Let's start bioc transition after this is done.
> 
> Please remove the moreinfo tag once you are ready.

Sure, thanks Graham!

-- 
Best,
Nilesh


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Bug#1010422: transition: r-api-bioc-3.15

2022-05-03 Thread Graham Inggs
Control: tags -1 + moreinfo

Hi Nilesh

On Tue, 3 May 2022 at 15:51, Nilesh Patra  wrote:
>
> Andreas Tille wrote:
> >> >I guess your recent upload of 0.1.2.1-3 is supposed to fix this and
> >> >is intended to enable the migration, right?
> >> >
> >>
> >> Yes, let's wait until r-base migrates, I guess it'd take a day or two 
> >> maybe.
> >> Anyway we need to wait for bioc transition until we get a thumbs up from 
> >> release team.
> >
> > Sure. I guess it is sensible to not fiddle around with R package
> > updates for the moment.
>
> I am now trying to get ggplot2 and friends in testing. Please give
> it time until this weekend to migrate after which I will remove
> my hacks and re-upload.

Please also look at rmatrix, it is a build-dependency of several
r-bioc-* packages.

> Let's start bioc transition after this is done.

Please remove the moreinfo tag once you are ready.

Regards
Graham



Bug#1010422: transition: r-api-bioc-3.15

2022-05-02 Thread Nilesh Patra



On 2 May 2022 11:54:34 am IST, Andreas Tille  wrote:
>Am Mon, May 02, 2022 at 09:39:25AM +0530 schrieb Nilesh Patra:
>> On Sun, 1 May 2022 11:42:07 +0200 =?UTF-8?B?RHlsYW4gQcOvc3Np?= 
>>  wrote:
>> > Hi,
>> > Bioconductor 3.15 has been released [1].
>> 
>> Please hold this off until r-base migrates (which should be soon)
>
>As far as I can see the testing migration is blocked by
>
>Isn't this the just discussed Graphics API issue?

There were many more of 'em blocking the transition. I cleaned that up 
yesterday and reduced it to the one remaining.

>I guess your recent upload of 0.1.2.1-3 is supposed to fix this and
>is intended to enable the migration, right?
>

Yes, let's wait until r-base migrates, I guess it'd take a day or two maybe.
Anyway we need to wait for bioc transition until we get a thumbs up from 
release team.

Migrating the graphics packages are also a mess now due to no-binNMUs. Need to 
propagate hacks to get these in testing. All of it could have been avoided if 
it was properly coordinated, but anyway.

>[1] 
>https://ci.debian.net/data/autopkgtest/testing/arm64/r/r-cran-thematic/21293099/log.gz
>

--
Best,
Nilesh



Bug#1010422: transition: r-api-bioc-3.15

2022-05-02 Thread Andreas Tille
Am Mon, May 02, 2022 at 09:39:25AM +0530 schrieb Nilesh Patra:
> On Sun, 1 May 2022 11:42:07 +0200 =?UTF-8?B?RHlsYW4gQcOvc3Np?= 
>  wrote:
> > Hi,
> > Bioconductor 3.15 has been released [1].
> 
> Please hold this off until r-base migrates (which should be soon)

As far as I can see the testing migration is blocked by

  ∙ autopkgtest for r-cran-thematic/0.1.2.1-2: amd64: Pass, arm64: Regression ♻ 
(reference ♻), armhf: Pass, i386: Pass, ppc64el: Pass, s390x: Pass

where the autopkgtest log[1] says:

...
══ Failed tests 
── Error (test-base.R:9:3): base baselines ─
Error in `svglite_(filename, bg, width, height, pointsize, standalone, 
always_valid)`: Graphics API version mismatch
Backtrace:
▆
 1. └─thematic:::expect_doppelganger(...) at test-base.R:9:2
 2.   └─vdiffr::expect_doppelganger(name, p, ...) at 
tests/testthat/helper-vdiffr.R:12:2
 3. └─vdiffr writer(fig, testcase, title)
 4.   └─vdiffr:::svglite(file)
 5. └─vdiffr:::svglite_(...)
── Error (test-ggplot.R:31:3): ggplot baselines 
Error in `svglite_(filename, bg, width, height, pointsize, standalone, 
always_valid)`: Graphics API version mismatch
Backtrace:
▆
 1. └─thematic:::expect_doppelganger(...) at test-ggplot.R:31:2
 2.   └─vdiffr::expect_doppelganger(name, p, ...) at 
tests/testthat/helper-vdiffr.R:12:2
 3. └─vdiffr writer(fig, testcase, title)
 4.   └─vdiffr:::svglite(file)
 5. └─vdiffr:::svglite_(...)
── Error (test-ggplot.R:149:3): Scale defaults can be overridden ───
Error in `svglite_(filename, bg, width, height, pointsize, standalone, 
always_valid)`: Graphics API version mismatch
...

Isn't this the just discussed Graphics API issue?

I guess your recent upload of 0.1.2.1-3 is supposed to fix this and
is intended to enable the migration, right?

Kind regards

  Andreas.


[1] 
https://ci.debian.net/data/autopkgtest/testing/arm64/r/r-cran-thematic/21293099/log.gz

-- 
http://fam-tille.de



Bug#1010422: transition: r-api-bioc-3.15

2022-05-01 Thread Nilesh Patra
On Sun, 1 May 2022 11:42:07 +0200 =?UTF-8?B?RHlsYW4gQcOvc3Np?= 
 wrote:
> Hi,
> Bioconductor 3.15 has been released [1].

Please hold this off until r-base migrates (which should be soon)

--
Best,
Nilesh


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Bug#1010422: transition: r-api-bioc-3.15

2022-05-01 Thread Dylan Aïssi
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: transition
X-Debbugs-CC: debia...@lists.debian.org


Hi,
Bioconductor 3.15 has been released [1].

[1] https://bioconductor.org/news/bioc_3_15_release/

Like for previous r-api-bioc transitions, all reverse dependencies
need a manual upgrade to the new upstream releases, they are not
binNMU-able. The Debian R Packages team will do so.

Please set up a tracker manually, since this is a transition of a
virtual package name.

Ben file:
-
title = "r-api-bioc-3.15";
is_affected = .depends ~ /r-api-bioc/;
is_good = .depends ~ "r-api-bioc-3.15";
is_bad = .depends ~ "r-api-bioc-3.14";
-

Best,
Dylan