Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Vladimir Dergachev]

On Wed, 1 Nov 2023, David Hugh-Jones wrote:


Aside from the package question, surely the other issue here is that Prof
Ripley’s email is extraordinarily rude. Any paid employee would be sacked
for that. I appreciate R and CRAN are volunteer-run organisations, but I
don’t think that should be an excuse for this level of, frankly, toxicity.
Why is he allowed to get away with it?


So one thing to keep in mind that doing volunteer public facing work tends 
to expose people to all kinds of unreasonable requests.


Those who endure often become more direct, and that's fine. Or, and 
people in commercial companies can be very direct too.


One thing that helps is to be extra-polite to a person who is doing a lot 
of volunteer work, and who is likely way oversubscribed.


Focusing on practical matters, if you take a step back things look 
pretty good:


Your package has dependency on a package that you have not written and
that is maintained outside CRAN. It was bound to break sooner or later.

However, the last time you updated bioOED was in 2019 and there was no 
need to do anything for more than 3 years. That's amazing ! And probably 
made possible by being a little bit too direct on occasion.


best

Vladimir Dergachev



David


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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[David Hugh-Jones]

Guys,

Martin, I am very sorry you spent all that time. I am sceptical that this
is a correct interpretation of the law, given what I see on Twitter daily,
and I would not take a university as an authority on this. But that is
neither here nor there – if I made you waste your time, that's my bad and
I'm sorry.

More generally, I have absolutely no wish to spend time beating up on any
individual – and people have kindly sent comments off-list that gave me
context about the specific case. But persistent rudeness is harmful, and
there ought to be a way to address it. Many projects use codes of conduct
for this purpose.

David


On Fri, 3 Nov 2023 at 11:15, Martin Maechler 
wrote:

> Dear R-package-devel readers *and* notably writers,
>
> In Europe there are (diverse) laws about privacy etc, and those,
> (and/or some politeness) do not allow
> free citing of private e-mail communications in public
> nor ad hominem remarks in such public communication.
>
> For this reason, I (as mailing list co-maintainer, and notably
> responsible for the lawfulness of the public mailing list archives on
> our web server) now spent about 2 hours  to carefully obey such
> privacy requirements (carefully editing + recreating all the html
> archives).
> {In another similar case, my employer, ETH Zurich, did urge me
> "from above" to spend my time with such a tedious and ungratifying job ...}
> This is *NOT* something I'd be happy to redo.
>
> So *please* do not misuse such a public mailing list and do keep
> your private opinions private in such a case in the future!
>
> > Spencer Graves  on Thu, 2 Nov 2023 15:29:29 -0500 writes:
>
> > On 11/2/23 2:52 PM, Rolf Turner wrote:
> >>
> >> On Wed, 1 Nov 2023 16:10:34 + David Hugh-Jones wrote:
> >>
> >>> Aside from the package question, surely the other issue
> >>> here is that ’s email is extraordinarily
> >>> rude. Any paid employee would be sacked for that. I
> >>> appreciate R and CRAN are volunteer-run organisations,
> >>> but I don’t think that should be an excuse for this
> >>> level of, frankly, toxicity. Why is he allowed to get
> >>> away with it?
> >>>
> >>> David
>
> >>
> >> I've just had a look at the initial posting in this
> >> thread
> >>
> >> and can see nothing rude or offensive in the email
> >> that was copied and pasted into that  posting.
> >>
> >> I find *your* email far more offensive than anything that
> >>  has ever written.  Get a life.
> >>
> >> cheers,
> >>
> >> Rolf Turner
> >>
> >> P.S.  See fortunes::fortune(88).
> >>
> >> R. T.
>
>
> > Hi, David:
>
>
> []
>
>
> > I've been in the military, and I've learned to ignore
> > the tone and look for the value in comments I
> > receive. I've learned a lot from , and
> > others. When the tone seemed less supportive or even
> > insulting, I'm very glad the person took the time to
> > comment and didn't decide not to reply for fear of
> > offending me. I'm more productive and a better human for
> > all the help I've gotten from this and other R-related
> > lists.
>
>
> > fortunes::fortune('Spencer Graves')
>
> which can you get 4 different answers; using `showMatches` argument
> (which I think I had added), e.g. now gives
>
> > fortune("Spencer Graves", showMatches = TRUE)
> Matching row numbers: 90, 124, 177, 271
>
> Rolf Turner: In the middle of a Saturday morning (in my Time Zone!) I send
> out a plea for help, and in
> just over 20 minutes my problem is solved!
> I don't think you get service like that anywhere else. This R-help list is
> BLOODY AMAZING!
> Spencer Graves: 'The sun never sets on the (former) British Empire.'
> Today, it never sets on R-Help.
>-- Rolf Turner and Spencer Graves
>   R-help (May 2005)
>
> and then
>
> > fortune(90)
>
> Our great-great grandchildren as yet unborn may read some of the stupid
> questions and/or answers that I
> and perhaps others give from time to time. I'd rather get flamed for
> saying something stupid in public on
> this list than to continue to provide substandard service to the people
> with whom I work because I
> perpetrated the same mistake in an environment in which no one questioned
> so effectively my errors.
>-- Spencer Graves (in a discussion on whether answers on R-help should
> be more polite)
>   R-help (December 2004)
>
> > sg
>
> Martin
>
>
> --
> Martin Maechler
> ETH Zurich  and  R Core team
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Martin Maechler]

Dear R-package-devel readers *and* notably writers,

In Europe there are (diverse) laws about privacy etc, and those,
(and/or some politeness) do not allow
free citing of private e-mail communications in public
nor ad hominem remarks in such public communication.

For this reason, I (as mailing list co-maintainer, and notably
responsible for the lawfulness of the public mailing list archives on
our web server) now spent about 2 hours  to carefully obey such
privacy requirements (carefully editing + recreating all the html archives).
{In another similar case, my employer, ETH Zurich, did urge me
"from above" to spend my time with such a tedious and ungratifying job ...}
This is *NOT* something I'd be happy to redo.

So *please* do not misuse such a public mailing list and do keep
your private opinions private in such a case in the future!

> Spencer Graves  on Thu, 2 Nov 2023 15:29:29 -0500 writes:

> On 11/2/23 2:52 PM, Rolf Turner wrote:
>> 
>> On Wed, 1 Nov 2023 16:10:34 + David Hugh-Jones wrote:
>> 
>>> Aside from the package question, surely the other issue
>>> here is that ’s email is extraordinarily
>>> rude. Any paid employee would be sacked for that. I
>>> appreciate R and CRAN are volunteer-run organisations,
>>> but I don’t think that should be an excuse for this
>>> level of, frankly, toxicity. Why is he allowed to get
>>> away with it?
>>> 
>>> David

>> 
>> I've just had a look at the initial posting in this
>> thread
>>
>> and can see nothing rude or offensive in the email
>> that was copied and pasted into that  posting.
>> 
>> I find *your* email far more offensive than anything that
>>  has ever written.  Get a life.
>> 
>> cheers,
>> 
>> Rolf Turner
>> 
>> P.S.  See fortunes::fortune(88).
>> 
>> R. T.


> Hi, David:


[]


> I've been in the military, and I've learned to ignore
> the tone and look for the value in comments I
> receive. I've learned a lot from , and
> others. When the tone seemed less supportive or even
> insulting, I'm very glad the person took the time to
> comment and didn't decide not to reply for fear of
> offending me. I'm more productive and a better human for
> all the help I've gotten from this and other R-related
> lists.


> fortunes::fortune('Spencer Graves')

which can you get 4 different answers; using `showMatches` argument
(which I think I had added), e.g. now gives

> fortune("Spencer Graves", showMatches = TRUE)
Matching row numbers: 90, 124, 177, 271 

Rolf Turner: In the middle of a Saturday morning (in my Time Zone!) I send out 
a plea for help, and in
just over 20 minutes my problem is solved!
I don't think you get service like that anywhere else. This R-help list is 
BLOODY AMAZING!
Spencer Graves: 'The sun never sets on the (former) British Empire.' Today, it 
never sets on R-Help.
   -- Rolf Turner and Spencer Graves
  R-help (May 2005)

and then

> fortune(90)

Our great-great grandchildren as yet unborn may read some of the stupid 
questions and/or answers that I
and perhaps others give from time to time. I'd rather get flamed for saying 
something stupid in public on
this list than to continue to provide substandard service to the people with 
whom I work because I
perpetrated the same mistake in an environment in which no one questioned so 
effectively my errors.
   -- Spencer Graves (in a discussion on whether answers on R-help should be 
more polite)
  R-help (December 2004)

> sg

Martin


--
Martin Maechler
ETH Zurich  and  R Core team

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Spencer Graves]

On 11/2/23 2:52 PM, Rolf Turner wrote:


On Wed, 1 Nov 2023 16:10:34 +
David Hugh-Jones  wrote:


Aside from the package question, surely the other issue here is that
Prof Ripley’s email is extraordinarily rude. Any paid employee would
be sacked for that. I appreciate R and CRAN are volunteer-run
organisations, but I don’t think that should be an excuse for this
level of, frankly, toxicity. Why is he allowed to get away with it?

David


I've just had a look at the initial posting in this thread

https://stat.ethz.ch/pipermail/r-package-devel/2023q4/009810.html

and can see nothing rude or offensive in the email from Prof. Ripley
that was copied and pasted into that posting.

I find *your* email far more offensive than anything that Prof. Ripley
has ever written.  Get a life.

cheers,

Rolf Turner

P.S.  See fortunes::fortune(88).

R. T.



Hi, David:


	  You do, of course, know that "Ripley" is a verb? People on this list 
take pride in how many times they've been Ripleyed ;-)



	  I've been in the military, and I've learned to ignore the tone and 
look for the value in comments I receive. I've learned a lot from 
Professor Ripley, and others. When the tone seemed less supportive or 
even insulting, I'm very glad the person took the time to comment and 
didn't decide not to reply for fear of offending me. I'm more productive 
and a better human for all the help I've gotten from this and other 
R-related lists.



fortunes::fortune('Spencer Graves')


  sg




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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Rolf Turner]

On Wed, 1 Nov 2023 16:10:34 +
David Hugh-Jones  wrote:

> Aside from the package question, surely the other issue here is that
> Prof Ripley’s email is extraordinarily rude. Any paid employee would
> be sacked for that. I appreciate R and CRAN are volunteer-run
> organisations, but I don’t think that should be an excuse for this
> level of, frankly, toxicity. Why is he allowed to get away with it?
> 
> David

I've just had a look at the initial posting in this thread

https://stat.ethz.ch/pipermail/r-package-devel/2023q4/009810.html

and can see nothing rude or offensive in the email from Prof. Ripley
that was copied and pasted into that posting.

I find *your* email far more offensive than anything that Prof. Ripley
has ever written.  Get a life.

cheers,

Rolf Turner

P.S.  See fortunes::fortune(88).

R. T.

-- 
Honorary Research Fellow
Department of Statistics
University of Auckland
Stats. Dep't. (secretaries) phone:
 +64-9-373-7599 ext. 89622
Home phone: +64-9-480-4619

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[David Hugh-Jones]

Aside from the package question, surely the other issue here is that Prof
Ripley’s email is extraordinarily rude. Any paid employee would be sacked
for that. I appreciate R and CRAN are volunteer-run organisations, but I
don’t think that should be an excuse for this level of, frankly, toxicity.
Why is he allowed to get away with it?

David

On Wed, 1 Nov 2023 at 11:15, Alberto Garre  wrote:

> Dear community,
>
> I feel dismay for having to write this email, but the issue must be brought
> up. On the 20th of October, I received an email from CRAN warning me of an
> issue with one of the packages I maintain (bioOED). The package depended on
> MEIGOR, a package that was no longer available in Bioconductor. I was given
> until 2023-11-03 to fix the issue.
>
> I contacted the MEIGOR maintainers and they told me they were migrating to
> CRAN. Yesterday, they contacted me again, telling me they needed more time
> for the migration. Hence, I responded to the email I received from CRAN,
> asking for an extension of the previous deadline (2023-11-03).
>
> To my surprise, it is not just that the extension was not granted, but the
> package has been removed from CRAN today (2023-11-01). Two days before the
> deadline (2023-11-03): https://cran.r-project.org/package=bioOED
>
> Then, I checked my inbox and I saw an email from one of the CRAN
> maintainers, showing that the package was removed because he had felt
> offended by my email. I copy-paste the email below.
>
> I understand that maintaining CRAN must be a huge work. I also work in
> academia, so I am totally aware of all the extra work that is required from
> us. But it is unreasonable that a package can be removed just because a
> maintainer throws a tantrum
>
> Again, I am really sorry I had to write this email, but CRAN cannot work if
> we allow this type of situation.
>
> Kind regards,
> Alberto Garre
>
> ## Mail from rip...@stats.ox.ac.uk on 2023-11-01 8:28
>
> On 31/10/2023 17:21, Alberto Garre wrote:
> > Dear Brian,
>
> Do be respectful whoever you are (you lack the manners to use a
> signature block but send HTML when you agreed not to!).  What exactly
> have you done for me that would allow you treat me as if I were your peer?
>
> Your ingratitude (for CRAN and R) is deafening.
>
> > I have talked to the MEIGOR developers and they need a bit more time to
> > update their package. Would it be possible to get a 4 weeks extension for
> > the update of bioOED?
>
> No one can even install it in current R, so it has been removed.
>
> "The time of the volunteers is CRAN’s most precious resource"
>
> Professor Ripley
>
> >
> > Thank you very much,
> > Alberto
> >
> >
> > El vie, 20 oct 2023 a las 9:24, Alberto Garre ( >)
> > escribió:
> >
> >> Thank you very much, Brian.
> >>
> >> I have just contacted the developers of MEIGOR because I think they were
> >> planning a migration to CRAN. I will update the package asap.
> >>
> >> Best,
> >> Alberto
> >>
> >>
> >> El vie, 20 oct 2023 a las 9:22, Prof Brian Ripley (<
> rip...@stats.ox.ac.uk
> >)
> >> escribió:
> >>
> >>> On 20/10/2023 08:17, Prof Brian Ripley wrote:
>  Dear maintainer,
> 
>  Please see the problems shown on
>  .
> 
>  Please correct before 2023-11-03 to safely retain your package on
> CRAN.
> 
>  The CRAN Team
> 
> >>> This requires package MEIGOR which is not part of BioC 3.18 and has
> been
> >>> deprecated so it very unlikely to be part of the final release next
> week.
> >>>
> >>>
> >>> --
> >>> Brian D. Ripley,  rip...@stats.ox.ac.uk
> >>> Emeritus Professor of Applied Statistics, University of Oxford
> >>>
> >>>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
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>
-- 
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Book: www.wyclifsdust.com

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Duncan Murdoch]

On 01/11/2023 2:54 p.m., Markus Jochim wrote:

Dear Alberto,

I have had a small number of CRAN-related email exchanges with Brian
Ripley that made it clear that his idea of politeness and my idea of
politeness are incompatible. The email you are quoting reminds me very
much of these exchanges.



My idea of politeness, and I think also Prof. Ripley's, is that you 
don't discuss private discussions in public without agreement from all 
parties.


Duncan Murdoch

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Markus Jochim]

Dear Alberto,

I have had a small number of CRAN-related email exchanges with Brian 
Ripley that made it clear that his idea of politeness and my idea of 
politeness are incompatible. The email you are quoting reminds me very 
much of these exchanges.


But I try to be pragmatic about it. It’s not the end of the world if my 
packages are not on CRAN for a couple of weeks. In the end, they were 
archived because tests were failing and they were always (re-)accepted 
into CRAN once the automatic tests passed again. No personal matters 
involved.


Brian Ripley has certainly contributed a lot to R. As a package 
maintainer, I am also contributing my share, especially towards my own 
discipline, and so are you. That is why there is contact in the first 
place. I wouldn't care too much whether or not that allows either of us 
to consider the other a peer.


I don’t know why your package appears to have been archived two days 
early. But otherwise I agree with Tomas and Duncan. There is a clear 
path forward for your package. Based on my own experience, there is no 
reason to believe that it will be rejected by CRAN on personal grounds, 
once the automatic tests pass.


Best

Markus

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Duncan Murdoch]

On 01/11/2023 8:35 a.m., Tomas Kalibera wrote:


On 11/1/23 12:15, Alberto Garre wrote:

Dear community,

I feel dismay for having to write this email, but the issue must be brought
up. On the 20th of October, I received an email from CRAN warning me of an
issue with one of the packages I maintain (bioOED). The package depended on
MEIGOR, a package that was no longer available in Bioconductor. I was given
until 2023-11-03 to fix the issue.

I contacted the MEIGOR maintainers and they told me they were migrating to
CRAN. Yesterday, they contacted me again, telling me they needed more time
for the migration. Hence, I responded to the email I received from CRAN,
asking for an extension of the previous deadline (2023-11-03).

To my surprise, it is not just that the extension was not granted, but the
package has been removed from CRAN today (2023-11-01). Two days before the
deadline (2023-11-03): https://cran.r-project.org/package=bioOED

Then, I checked my inbox and I saw an email from one of the CRAN
maintainers, showing that the package was removed because he had felt
offended by my email. I copy-paste the email below.


I don't think this is true. The reason is that your package depends on
an unavailable package, so cannot be installed. See
https://cran.r-project.org/web/packages/bioOED/index.html where the
reason is publicly stated.

If I were you I'd simply wait once MEIGOR is on CRAN and then publish
the archived package again.


I agree with that interpretation.  A possibly faster alternative would 
be to remove the dependence on MEIGOR, and resubmit once that is done 
and the package is working again.


Duncan Murdoch

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Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Tomas Kalibera]

On 11/1/23 12:15, Alberto Garre wrote:

Dear community,

I feel dismay for having to write this email, but the issue must be brought
up. On the 20th of October, I received an email from CRAN warning me of an
issue with one of the packages I maintain (bioOED). The package depended on
MEIGOR, a package that was no longer available in Bioconductor. I was given
until 2023-11-03 to fix the issue.

I contacted the MEIGOR maintainers and they told me they were migrating to
CRAN. Yesterday, they contacted me again, telling me they needed more time
for the migration. Hence, I responded to the email I received from CRAN,
asking for an extension of the previous deadline (2023-11-03).

To my surprise, it is not just that the extension was not granted, but the
package has been removed from CRAN today (2023-11-01). Two days before the
deadline (2023-11-03): https://cran.r-project.org/package=bioOED

Then, I checked my inbox and I saw an email from one of the CRAN
maintainers, showing that the package was removed because he had felt
offended by my email. I copy-paste the email below.


I don't think this is true. The reason is that your package depends on 
an unavailable package, so cannot be installed. See 
https://cran.r-project.org/web/packages/bioOED/index.html where the 
reason is publicly stated.


If I were you I'd simply wait once MEIGOR is on CRAN and then publish 
the archived package again.


Best,
Tomas



I understand that maintaining CRAN must be a huge work. I also work in
academia, so I am totally aware of all the extra work that is required from
us. But it is unreasonable that a package can be removed just because a
maintainer throws a tantrum

Again, I am really sorry I had to write this email, but CRAN cannot work if
we allow this type of situation.

Kind regards,
Alberto Garre

## Mail from rip...@stats.ox.ac.uk on 2023-11-01 8:28

On 31/10/2023 17:21, Alberto Garre wrote:

Dear Brian,

Do be respectful whoever you are (you lack the manners to use a
signature block but send HTML when you agreed not to!).  What exactly
have you done for me that would allow you treat me as if I were your peer?

Your ingratitude (for CRAN and R) is deafening.


I have talked to the MEIGOR developers and they need a bit more time to
update their package. Would it be possible to get a 4 weeks extension for
the update of bioOED?

No one can even install it in current R, so it has been removed.

"The time of the volunteers is CRAN’s most precious resource"

Professor Ripley


Thank you very much,
Alberto


El vie, 20 oct 2023 a las 9:24, Alberto Garre ()
escribió:


Thank you very much, Brian.

I have just contacted the developers of MEIGOR because I think they were
planning a migration to CRAN. I will update the package asap.

Best,
Alberto


El vie, 20 oct 2023 a las 9:22, Prof Brian Ripley (
)

escribió:


On 20/10/2023 08:17, Prof Brian Ripley wrote:

Dear maintainer,

Please see the problems shown on
.

Please correct before 2023-11-03 to safely retain your package on CRAN.

The CRAN Team


This requires package MEIGOR which is not part of BioC 3.18 and has been
deprecated so it very unlikely to be part of the final release next

week.


--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford



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[R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

[Alberto Garre]

Dear community,

I feel dismay for having to write this email, but the issue must be brought
up. On the 20th of October, I received an email from CRAN warning me of an
issue with one of the packages I maintain (bioOED). The package depended on
MEIGOR, a package that was no longer available in Bioconductor. I was given
until 2023-11-03 to fix the issue.

I contacted the MEIGOR maintainers and they told me they were migrating to
CRAN. Yesterday, they contacted me again, telling me they needed more time
for the migration. Hence, I responded to the email I received from CRAN,
asking for an extension of the previous deadline (2023-11-03).

To my surprise, it is not just that the extension was not granted, but the
package has been removed from CRAN today (2023-11-01). Two days before the
deadline (2023-11-03): https://cran.r-project.org/package=bioOED

Then, I checked my inbox and I saw an email from one of the CRAN
maintainers, showing that the package was removed because he had felt
offended by my email. I copy-paste the email below.

I understand that maintaining CRAN must be a huge work. I also work in
academia, so I am totally aware of all the extra work that is required from
us. But it is unreasonable that a package can be removed just because a
maintainer throws a tantrum

Again, I am really sorry I had to write this email, but CRAN cannot work if
we allow this type of situation.

Kind regards,
Alberto Garre

## Mail from rip...@stats.ox.ac.uk on 2023-11-01 8:28

On 31/10/2023 17:21, Alberto Garre wrote:
> Dear Brian,

Do be respectful whoever you are (you lack the manners to use a
signature block but send HTML when you agreed not to!).  What exactly
have you done for me that would allow you treat me as if I were your peer?

Your ingratitude (for CRAN and R) is deafening.

> I have talked to the MEIGOR developers and they need a bit more time to
> update their package. Would it be possible to get a 4 weeks extension for
> the update of bioOED?

No one can even install it in current R, so it has been removed.

"The time of the volunteers is CRAN’s most precious resource"

Professor Ripley

>
> Thank you very much,
> Alberto
>
>
> El vie, 20 oct 2023 a las 9:24, Alberto Garre ()
> escribió:
>
>> Thank you very much, Brian.
>>
>> I have just contacted the developers of MEIGOR because I think they were
>> planning a migration to CRAN. I will update the package asap.
>>
>> Best,
>> Alberto
>>
>>
>> El vie, 20 oct 2023 a las 9:22, Prof Brian Ripley ()
>> escribió:
>>
>>> On 20/10/2023 08:17, Prof Brian Ripley wrote:
 Dear maintainer,

 Please see the problems shown on
 .

 Please correct before 2023-11-03 to safely retain your package on CRAN.

 The CRAN Team

>>> This requires package MEIGOR which is not part of BioC 3.18 and has been
>>> deprecated so it very unlikely to be part of the final release next
week.
>>>
>>>
>>> --
>>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
>>>
>>>

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