Hi
On 18-12-2023 10:07, Andreas Tille wrote:
https://tracker.debian.org/pkg/r-bioc-megadepth
d/tests/control has
Architecture: !s390x
Why is it considered failing on s390x anyway?
The log has this at the end:
127s run-unit-testSKIP Test declares architecture as not
supported:
Hi Graham,
Am Sun, Dec 17, 2023 at 02:11:47PM -0100 schrieb Graham Inggs:
> There are some packages that have still not migrated since the
> previous r-api-bioc-3.17 transition in July 2023.
>
> Links to their tracker pages, which should tell you what is needed, follow:
>
>
Hi Andreas
There are some packages that have still not migrated since the
previous r-api-bioc-3.17 transition in July 2023.
Links to their tracker pages, which should tell you what is needed, follow:
https://tracker.debian.org/pkg/r-bioc-cner
https://tracker.debian.org/pkg/r-bioc-dada2
Hi Paul,
Am Wed, Dec 13, 2023 at 09:56:14PM +0100 schrieb Paul Gevers:
> > > Not built on buildd: arch all binaries uploaded by tille, a new
> > > source-only upload is needed to allow migration
> >
> > I do not understand this line. What exact package needs a source-only
> > upload?
>
> You
Hi,
On 13-12-2023 17:08, Andreas Tille wrote:
Not built on buildd: arch all binaries uploaded by tille, a new
source-only upload is needed to allow migration
I do not understand this line. What exact package needs a source-only
upload?
You uploaded binaries together with the source.
Hi Graham,
Am Wed, Dec 13, 2023 at 12:13:54PM -0100 schrieb Graham Inggs:
> I've added removal hints for r-bioc-dss and r-bioc-demixt. Please
> file an RC bug for r-bioc-dss to prevent it from migrating straight
> back (r-bioc-demixt already has #1058278).
Done for r-bioc-dss.
> One problem I
Hi Andreas
On Wed, 13 Dec 2023 at 09:45, Andreas Tille wrote:
> as you might have noticed the upstream source for r-bioc-dss and
> r-bioc-demixt are missing and upstream did not answered two mails about
> this. Since the transition looks clean for me so far[1] after I fixed
> two autopkgtest
On Wed, Dec 13, 2023 at 11:43:56AM +0100, Andreas Tille wrote:
>...
> I'm worried
> about issues in r-rcan-rmarkdown[3] and r-cran-flextable[4] which are
> caused by pandoc errors on ppc64el architecture *only*. That's really
> strange and might mean that pandoc on this architecture is broken?
Hi,
as you might have noticed the upstream source for r-bioc-dss and
r-bioc-demixt are missing and upstream did not answered two mails about
this. Since the transition looks clean for me so far[1] after I fixed
two autopkgtest issues yesterday I (naively) think we could remove
r-bioc-dss and
On 2023-12-11 16:57:34 +0100, Andreas Tille wrote:
> Am Mon, Dec 11, 2023 at 01:36:38PM +0100 schrieb Sebastian Ramacher:
> > > OK, but what is your suggestion? Reverting and have broken tests due to
> > > the pandoc issue?
> >
> > pandoc is fixed in unstable.
>
> Really? Salsa CI[1] says:
>
Am Mon, Dec 11, 2023 at 01:36:38PM +0100 schrieb Sebastian Ramacher:
> > OK, but what is your suggestion? Reverting and have broken tests due to
> > the pandoc issue?
>
> pandoc is fixed in unstable.
Really? Salsa CI[1] says:
pandoc : Depends: pandoc-data (>= 3.0.1+ds) but 3.0.1-3 is to be
On 2023-12-11 13:28:59 +0100, Andreas Tille wrote:
> Hi Sebastian,
>
> Am Mon, Dec 11, 2023 at 11:29:24AM +0100 schrieb Sebastian Ramacher:
> > > > I found a workaround; demote pandoc from a Depends to a Recommends in
> > > > the r-cran-rmarkdown package. It seems that pandoc is not used for
> >
Hi Sebastian,
Am Mon, Dec 11, 2023 at 11:29:24AM +0100 schrieb Sebastian Ramacher:
> > > I found a workaround; demote pandoc from a Depends to a Recommends in
> > > the r-cran-rmarkdown package. It seems that pandoc is not used for
> > > building, at least for r-bioc-biovizbase, -degnorm,
Hi Andreas
On 2023-12-07 16:09:28 +0100, Andreas Tille wrote:
> Hi Graham,
>
> Am Thu, Dec 07, 2023 at 01:37:02PM -0100 schrieb Graham Inggs:
> > On Sun, 3 Dec 2023 at 07:21, Andreas Tille wrote:
> > > I have no idea how to work around this.
> >
> > I found a workaround; demote pandoc from a
On 9 December 2023 at 01:06, Charles Plessy wrote:
| I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar
| packages, it is because it is an "annotation package" made of data and
| therefore not managed the same way as the other Bioconductor packages.
|
| This is why it
Hi Graham and Andreas,
Le Thu, Dec 07, 2023 at 01:37:02PM -0100, Graham Inggs a écrit :
>
> Also, why do r-bioc-netsam and r-bioc-org.hs.eg.db not even appear on
> the tracker?
I do not know for r-bioc-netsam, but for r-bioc-org.hs.eg.db and similar
packages, it is because it is an "annotation
On Thu, Dec 07, 2023 at 04:09:28PM +0100, Andreas Tille wrote:
>...
> Am Thu, Dec 07, 2023 at 01:37:02PM -0100 schrieb Graham Inggs:
>...
> > Also, why do r-bioc-netsam and r-bioc-org.hs.eg.db not even appear on
> > the tracker?
>
> I was always wondering about this but I have no clue.
Am Thu, Dec 07, 2023 at 04:09:28PM +0100 schrieb Andreas Tille:
> I'll take this
> occurence as a reason to fail with an error in dh-r to avoid such cases
> in future.
Done in
https://salsa.debian.org/r-pkg-team/dh-r/-/commit/e4c348832b3d99ba7bc8f7670085b9b21323f7b6
The check could be even
Hi Graham,
Am Thu, Dec 07, 2023 at 01:37:02PM -0100 schrieb Graham Inggs:
> On Sun, 3 Dec 2023 at 07:21, Andreas Tille wrote:
> > I have no idea how to work around this.
>
> I found a workaround; demote pandoc from a Depends to a Recommends in
> the r-cran-rmarkdown package. It seems that
Hi Andreas
On Sun, 3 Dec 2023 at 07:21, Andreas Tille wrote:
> I have no idea how to work around this.
I found a workaround; demote pandoc from a Depends to a Recommends in
the r-cran-rmarkdown package. It seems that pandoc is not used for
building, at least for r-bioc-biovizbase, -degnorm,
On 2023-12-03 23:14:03 +0200, Adrian Bunk wrote:
> On Sun, Dec 03, 2023 at 09:46:31AM -0100, Graham Inggs wrote:
> >...
> > This is probably a good example for why new packages should be
> > uploaded to experimental first, instead of directly to unstable.
> >...
>
> Not really.
>
> It is rare
Hi Adrian,
Am Sun, Dec 03, 2023 at 11:15:49PM +0200 schrieb Adrian Bunk:
> > And it also means that r-bioc-biocgenerics is now blocked on the haskell
> > transition. Lovely. Good thing that pandoc is supposed to be the last piece
> > in that several months long transition.
>
> It's only blocked
Hi,
Am Sun, Dec 03, 2023 at 09:51:38PM +0100 schrieb Paul Gevers:
>
> And it also means that r-bioc-biocgenerics is now blocked on the haskell
> transition. Lovely. Good thing that pandoc is supposed to be the last piece
> in that several months long transition.
... which on the other hand
On Sun, Dec 03, 2023 at 09:51:38PM +0100, Paul Gevers wrote:
>...
> And it also means that r-bioc-biocgenerics is now blocked on the haskell
> transition. Lovely. Good thing that pandoc is supposed to be the last piece
> in that several months long transition.
It's only blocked by the pandoc part
On Sun, Dec 03, 2023 at 09:46:31AM -0100, Graham Inggs wrote:
>...
> This is probably a good example for why new packages should be
> uploaded to experimental first, instead of directly to unstable.
>...
Not really.
It is rare that a new source package takes over a binary package from
another
Hi,
On 03-12-2023 11:46, Graham Inggs wrote:
This seems to be due to the restructuring of src:pandoc [1].
src:haskell-pandoc [2] recently cleared NEW into unstable, and the
updated src:pandoc has not been uploaded yet.
This is probably a good example for why new packages should be
uploaded to
Hi Andreas
On Sun, 3 Dec 2023 at 07:21, Andreas Tille wrote:
> Charles Plessy and I uploaded r-bioc-* packages until level 11.
> Unfortunately building of some packages seems to be blocked for
>
> A: some pandoc dependency reason
> pandoc depends on missing:
> -
Hi,
Charles Plessy and I uploaded r-bioc-* packages until level 11.
Unfortunately building of some packages seems to be blocked for
A: some pandoc dependency reason
pandoc depends on missing:
- pandoc-data:amd64 (< 2.17.1.1-3.~)
Am Tue, Nov 28, 2023 at 09:22:18AM +0900 schrieb Charles Plessy:
> would it be possible to have an estimation about when we can expect to
> start the Bioconductor transition ? I am contributing to Debian mostly
> on my work time and it would be super useful for me to have this
> information in
Le Wed, Nov 22, 2023 at 08:46:17PM +0100, Andreas Tille a écrit :
> Control: tags -1 - moreinfo
>
> r-bioc-sparsearray is accepted in unstable.
Hello everybody,
would it be possible to have an estimation about when we can expect to
start the Bioconductor transition ? I am contributing to
Hi Paul,
Am Fri, Nov 24, 2023 at 11:17:34AM +0100 schrieb Paul Gevers:
> On Wed, 22 Nov 2023 20:46:17 +0100 Andreas Tille wrote:
> > Control: tags -1 - moreinfo
> >
> > r-bioc-sparsearray is accepted in unstable.
>
> Well, Graham wrote "remove the 'moreinfo' tag once SparseArray has cleared
>
Hi Andreas,
On Wed, 22 Nov 2023 20:46:17 +0100 Andreas Tille wrote:
Control: tags -1 - moreinfo
r-bioc-sparsearray is accepted in unstable.
Well, Graham wrote "remove the 'moreinfo' tag once SparseArray has
cleared NEW, and rmatrix has migrated."
^^^
Note the "and".
We're
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Bug #1054657 [release.debian.org] transition: r-bioc-biocgenerics
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r-bioc-sparsearray is accepted in unstable.
Kind regards
Andreas.
--
http://fam-tille.de
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Hi Andreas
On Mon, 13 Nov 2023 at 09:10, Andreas Tille wrote:
> Thanks to the hint from Charles I found that SparseArray is not new in
> Bioconductor and we can build the previous version with the current
> packages in unstable which I did and uploaded to new.
Am Fri, Nov 10, 2023 at 11:26:21PM +0100 schrieb Andreas Tille:
>
> What about a compromise. We start the transition, r-bioc-s4arrays is in
> ...
Thanks to the hint from Charles I found that SparseArray is not new in
Bioconductor and we can build the previous version with the current
packages
Le Fri, Nov 10, 2023 at 11:30:13PM +0100, Sebastian Ramacher a écrit :
>
> Can you please clarify whether you are talking about new dependencies or
> reverse dependencies above? Thanks.
Hi Sebastian,
I am talking about the reverse-dependencies of the packages that we need
to upload to NEW.
On 2023-11-10 17:43:43 +0900, Charles Plessy wrote:
> Hi Paul and everybody,
>
> we are finding a way to compare the R dependencies of the Bioconductor
> packages in Debian and in Bioc 3.18. It uncovers some core packages
> introduced in Bioc 3.17, but which only start to have
>
Hi Paul,
Am Fri, Nov 10, 2023 at 08:39:18PM +0100 schrieb Paul Gevers:
> On 10-11-2023 11:56, Andreas Tille wrote:
> > The only new dependency we need is SparseArray. However, we cannot
> > upload the package to new since it needs r-bioc-s4arrays (>= 1.1.6) for
> > building it. In other words:
Hi,
On 10-11-2023 11:56, Andreas Tille wrote:
The only new dependency we need is SparseArray. However, we cannot
upload the package to new since it needs r-bioc-s4arrays (>= 1.1.6) for
building it. In other words: We need to start the transition before we
can package SparseArray.
You're
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Hi,
Am Fri, Nov 10, 2023 at 05:43:43PM +0900 schrieb Charles Plessy:
> Hi Paul and everybody,
I admit Paul's mail was convincing enough to dive deeper into this. I
also need to admit that hacking together some scripts doing the job was
less effort than I expected,
Hi Paul and everybody,
we are finding a way to compare the R dependencies of the Bioconductor
packages in Debian and in Bioc 3.18. It uncovers some core packages
introduced in Bioc 3.17, but which only start to have
reverse-dependencies in 3.18, meaning that they are not in Debian yet
since we
Le Thu, Nov 09, 2023 at 02:01:57PM +0100, Paul Gevers a écrit :
>
> The first and foremost reason why we're not enthusiastic about defaulting to
> removal of packages from testing is that that's a disservice to our users of
> testing.
Hi Paul,
I understand that you feel responsible for the
Hi Andreas,
On 07-11-2023 18:01, Andreas Tille wrote:
You did not yet answered the question I asked twice whether we can find
a compromise by simply removing packages with missing new dependencies
from testing. I consider this a compromise which I would really love to
discuss honestly.
I'll
Hi Dirk,
Am Tue, Nov 07, 2023 at 12:28:22PM -0600 schrieb Dirk Eddelbuettel:
>
> "Kinda. Sorta. Not fully." I have written related code doing most of this
> during the many attempt for 'turning CRAN into .deb packages'.
> ...
Sounds like another idea how this problem can be turned into code
On 7 November 2023 at 14:58, Andreas Tille wrote:
| Do you see any way to answer the question that is discussed in this
| thread by r2u how to know whether new Bioconductor packages might have
| new dependencies not yet packaged for Debian?
"Kinda. Sorta. Not fully." I have written related code
Hi Sebastian,
Am Tue, Nov 07, 2023 at 03:12:39PM +0100 schrieb Sebastian Ramacher:
> > Charles and I tried to explain in different ways: We do not have simple
> > means to answer this question.
>
> Picking a random r-bioc-* package:
>
On 2023-11-07 14:38:13 +0100, Andreas Tille wrote:
> Hi Sebastian,
>
> Am Tue, Nov 07, 2023 at 10:53:00AM +0100 schrieb Sebastian Ramacher:
> > Control: tags -1 moreinfo
>
> I admit I'm not really happy about the bug ping-pong.
>
> > > I just finished inspecting by eye the homepage of each of
Hi Dirk,
Am Tue, Nov 07, 2023 at 07:40:38AM -0600 schrieb Dirk Eddelbuettel:
>
> On 7 November 2023 at 22:01, Charles Plessy wrote:
> | One possible direction would be to leverage the work done by Dirk and
> | others in r2u, where the Bioc transition is over, and for each package
> | in Debian,
On 7 November 2023 at 22:01, Charles Plessy wrote:
| One possible direction would be to leverage the work done by Dirk and
| others in r2u, where the Bioc transition is over, and for each package
| in Debian, look if the r2u equivalent has a dependency not in Debian.
|
|
Hi Sebastian,
Am Tue, Nov 07, 2023 at 10:53:00AM +0100 schrieb Sebastian Ramacher:
> Control: tags -1 moreinfo
I admit I'm not really happy about the bug ping-pong.
> > I just finished inspecting by eye the homepage of each of the 69 new
> > Bioconductor packages. None of them declare a
Le Tue, Nov 07, 2023 at 10:53:00AM +0100, Sebastian Ramacher a écrit :
>
> We do not care about new reverse dependencies.
Hi Sebastian,
I am sorry that the information that I sent appears to have wasted your
time. I still think that it does have some relevance, but I probably
did not explain
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Hi Charles
On 2023-11-03 09:56:13 +0900, Charles Plessy wrote:
> > Am Wed, Nov 01, 2023 at 09:02:10AM -0100 schrieb Graham Inggs:
> > > Again, we are not asking for the entire transition to happen in
> > > experimental. We are only asking for the NEW packages, so that
Control: tags -1 - moreinfo
Removing moreinfo tag since according to the investigation of Charles
gave some data points that we do not expect any new Bioconductor
packages (while we did not checked for any new CRAN packages.)
If this is not sufficient please be so kind to explain the problem of
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> Am Wed, Nov 01, 2023 at 09:02:10AM -0100 schrieb Graham Inggs:
> > Again, we are not asking for the entire transition to happen in
> > experimental. We are only asking for the NEW packages, so that NEW
> > processing happens before the transition, and not during.
Le Wed, Nov 01, 2023 at
Hi Graham,
Am Wed, Nov 01, 2023 at 09:02:10AM -0100 schrieb Graham Inggs:
> > Sorry, my question was probably confusing. I was not talking about the
> > new packages. I was talking about the 170 r-bioc-* packages. If I
> > upload these to experimental, will it be necessary to upload these to
>
HI Andreas
On Sun, 29 Oct 2023 at 16:06, Andreas Tille wrote:
> Sorry, my question was probably confusing. I was not talking about the
> new packages. I was talking about the 170 r-bioc-* packages. If I
> upload these to experimental, will it be necessary to upload these to
> unstable again
Le Sun, Oct 29, 2023 at 02:57:01PM -0100, Graham Inggs a écrit :
>
> No, after the NEW packages have cleared NEW and the moreinfo tag is
> removed, we'll consider a slot for the transition. We would like to
> avoid stalling the transition with multiple packages going through
> NEW, and putting
Hi Graham,
Am Sun, Oct 29, 2023 at 02:57:01PM -0100 schrieb Graham Inggs:
> Hi Andreas
>
> On Sun, 29 Oct 2023 at 04:33, Andreas Tille wrote:
> > Can you confirm that packages uploaded to experimental can be moved in
> > one rush from experimental to unstable without extra uploads?
>
> I don't
Hi Andreas
On Sun, 29 Oct 2023 at 04:33, Andreas Tille wrote:
> Can you confirm that packages uploaded to experimental can be moved in
> one rush from experimental to unstable without extra uploads?
I don't think this has ever been possible. The packages would need to
be uploaded again to
Hi Graham,
Am Sat, Oct 28, 2023 at 04:55:24PM + schrieb Graham Inggs:
>
> Please remove the 'moreinfo' tag once all NEW packages needed for this
> transition have been uploaded to experimental and have passed through
> NEW review.
Can you confirm that packages uploaded to experimental can
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Bug #1054657 [release.debian.org] transition: r-bioc-biocgenerics
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Hi Andreas
On Fri, 27 Oct 2023 at 14:03, Andreas Tille wrote:
> The BioConductor transition will bump the virtual package
> r-api-bioc-3.17 to r-api-bioc-3.18.
>
> BTW, I'm aware that a couple of r-bioc-* packages did not yet migrated
> to testing due to some
On 27 October 2023 at 16:43, Andreas Tille wrote:
| Am Fri, Oct 27, 2023 at 09:19:22AM -0500 schrieb Dirk Eddelbuettel:
| >
| > | BioConductor has just released version 3.17. Since the next r-base
| >
| > Typo: 3.18
|
| Yes. Thanks for pointing this out.
|
| > | release is pending on
Am Fri, Oct 27, 2023 at 09:19:22AM -0500 schrieb Dirk Eddelbuettel:
>
> | BioConductor has just released version 3.17. Since the next r-base
>
> Typo: 3.18
Yes. Thanks for pointing this out.
> | release is pending on 2023-10-31 we do not think it is a good idea to
> | start the transition
On 27 October 2023 at 16:00, Andreas Tille wrote:
| Package: release.debian.org
| Severity: normal
| User: release.debian@packages.debian.org
| Usertags: transition
| X-Debbugs-Cc: r-bioc-biocgener...@packages.debian.org,
debia...@lists.debian.org
| Control: affects -1 +
Package: release.debian.org
Severity: normal
User: release.debian@packages.debian.org
Usertags: transition
X-Debbugs-Cc: r-bioc-biocgener...@packages.debian.org, debia...@lists.debian.org
Control: affects -1 + src:r-bioc-biocgenerics
Hi,
BioConductor has just released version 3.17. Since
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