Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Henrik Bengtsson 
On Thu, Apr 18, 2024 at 6:41 AM Uwe Ligges
 wrote:
>
> On 18.04.2024 15:35, Ben Bolker wrote:
> > Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN
> > has apparently just caught up to checking.  What's a little frustrating
> > (to me) is that the dependence of prediction on ffbase is *very* soft
> > ("enhances") ...
>
> No, but CRAN  has still not received an update and asked for this each
> month this year, so in Jan, Feb, and March without a response, so we
> assume prediction is unmaintained. Also, this was escalated to reverse
> depends.

Uwe, has the CRAN Team ever considered making these request-for-update
email messages from CRAN public in real-time? For instance, there
could be a public "read-only" mailing list that anyone can subscribe
to, but not send/reply to. I see several advantages with such an
approach, e.g.

* maintainers of reverse dependencies would be aware of potential
problems much sooner,
* so would end-users who rely on the package (who often only notice
when a package is archived),
* the community could early on offer their help to the package maintainer, and
* the community could help locate and notify maintainers whose email
addresses are no longer working.

I'd imagine this would help lower the workload on the CRAN Team, so a
win-win for everyone. I, for sure, would find that useful.

Thanks,

Henrik

>> Best,
> Uwe Ligges
>
>
> >
> > On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
> >> The cascade is even longer. prediction got archived because ffbase was
> >> no longer available. https://cran.r-project.org/web/packages/ffbase/
> >> 
> >>
> >> ir. Thierry Onkelinx
> >> Statisticus / Statistician
> >>
> >> Vlaamse Overheid / Government of Flanders
> >> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> >> AND FOREST
> >> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> >> thierry.onkel...@inbo.be 
> >> Havenlaan 88 bus 73, 1000 Brussel
> >> *Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
> >> /Poststukken die naar dit adres worden gestuurd, worden ingescand en
> >> digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar
> >> dossiers volledig digitaal behandelen. Poststukken met de vermelding
> >> ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de
> >> geadresseerde bezorgd./
> >> www.inbo.be 
> >>
> >> ///
> >> To call in the statistician after the experiment is done may be no
> >> more than asking him to perform a post-mortem examination: he may be
> >> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> >> The plural of anecdote is not data. ~ Roger Brinner
> >> The combination of some data and an aching desire for an answer does
> >> not ensure that a reasonable answer can be extracted from a given body
> >> of data. ~ John Tukey
> >> ///
> >>
> >> 
> >>
> >>
> >> Op do 18 apr 2024 om 15:25 schreef Ben Bolker  >> >:
> >>
> >> Thank you! (I know about package_dependencies() but ran into
> >> precisely the same problem and didn't want to re-implement it ...)
> >>
> >> On 2024-04-18 9:11 a.m., Josiah Parry wrote:
> >>  > Well, after trying to install the package, I believe the issue is
> >>  > because margins has been archived.
> >>  >
> >>  > https://cran.r-project.org/web/packages/margins/index.html
> >> 
> >>  >  >> >
> >>  >
> >>  > You can check recursive dependencies using
> >>  > `tools::package_dependencies("pkg", recursive = TRUE)` which
> >> would help
> >>  > you in this case. I couldn't run it since the package is not
> >> available
> >>  > on CRAN, however.
> >>  >
> >>  >
> >>  > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker  >> 
> >>  > >> wrote:
> >>  >
> >>  > The 'dotwhisker' package was archived on CRAN: from
> >>  > https://cran.r-project.org/web/packages/dotwhisker/index.html
> >> 
> >>  >
> >>   >> >
> >>  >
> >>  >   Package ‘dotwhisker’ was removed from the CRAN
> >> repository
> >>  >   ...
> >>  >
> >>  >   Archived on 2024-04-12 as requires archived package
> >> 'prediction'.
> >>  >
> >>  >

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Uwe Ligges 



On 18.04.2024 15:48, Uwe Ligges wrote:



On 18.04.2024 15:43, Ben Bolker wrote:

  To clarify, from an off-list conversation:

   AFAICT the chain is

   dotwhisker Imports
  margins, which Imports
    prediction, which Enhances
  ffbase  (archived in 2022 for 'coercion to logical' problems)

  (that conversation also pointed out that Enhances is a dependency 
*in the opposite direction* -- i.e. if A Enhances B, it's not entirely 
clear why the disappearance of B should matter at all ...)


The year old check notes in prediciton matter, not the level of any 
dependencies.


.. and even more the non-maintainance state of prediction.

Best,
Uwe Ligges




Best,
Uwe Ligges








On 2024-04-18 9:35 a.m., Ben Bolker wrote:
    Yes, but ffbase was archived a long time ago (2022-04-04) and 
CRAN has apparently just caught up to checking.  What's a little 
frustrating (to me) is that the dependence of prediction on ffbase is 
*very* soft ("enhances") ...


On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
The cascade is even longer. prediction got archived because ffbase 
was no longer available. 
https://cran.r-project.org/web/packages/ffbase/ 



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR 
NATURE AND FOREST

Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be 
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
/Poststukken die naar dit adres worden gestuurd, worden ingescand en 
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid 
haar dossiers volledig digitaal behandelen. Poststukken met de 
vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan 
de geadresseerde bezorgd./

www.inbo.be 

///
To call in the statistician after the experiment is done may be no 
more than asking him to perform a post-mortem examination: he may be 
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does 
not ensure that a reasonable answer can be extracted from a given 
body of data. ~ John Tukey

///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker >:


    Thank you! (I know about package_dependencies() but ran into
    precisely the same problem and didn't want to re-implement it ...)

    On 2024-04-18 9:11 a.m., Josiah Parry wrote:
 > Well, after trying to install the package, I believe the 
issue is

 > because margins has been archived.
 >
 > https://cran.r-project.org/web/packages/margins/index.html
    
 > >
 >
 > You can check recursive dependencies using
 > `tools::package_dependencies("pkg", recursive = TRUE)` which
    would help
 > you in this case. I couldn't run it since the package is not
    available
 > on CRAN, however.
 >
 >
 > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker mailto:bbol...@gmail.com>
 > >> wrote:
 >
 >         The 'dotwhisker' package was archived on CRAN: from
 > https://cran.r-project.org/web/packages/dotwhisker/index.html
    
 >  >
 >
 >           Package ‘dotwhisker’ was removed from the CRAN 
repository

 >           ...
 >
 >           Archived on 2024-04-12 as requires archived package
    'prediction'.
 >
 >          However, I can't for the life of me see where this
    dependence
 >     could
 >     come from. Neither the DESCRIPTION file of the last-archived
    version on
 >     CRAN
 > 
  >>,

 >     nor the version on github
    
 >     >>, seem to
 >     show an

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Uwe Ligges 



On 18.04.2024 15:43, Ben Bolker wrote:

  To clarify, from an off-list conversation:

   AFAICT the chain is

   dotwhisker Imports
  margins, which Imports
    prediction, which Enhances
  ffbase  (archived in 2022 for 'coercion to logical' problems)

  (that conversation also pointed out that Enhances is a dependency *in 
the opposite direction* -- i.e. if A Enhances B, it's not entirely clear 
why the disappearance of B should matter at all ...)


The year old check notes in prediciton matter, not the level of any 
dependencies.


Best,
Uwe Ligges








On 2024-04-18 9:35 a.m., Ben Bolker wrote:
    Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN 
has apparently just caught up to checking.  What's a little 
frustrating (to me) is that the dependence of prediction on ffbase is 
*very* soft ("enhances") ...


On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
The cascade is even longer. prediction got archived because ffbase 
was no longer available. 
https://cran.r-project.org/web/packages/ffbase/ 



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR 
NATURE AND FOREST

Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be 
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
/Poststukken die naar dit adres worden gestuurd, worden ingescand en 
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid 
haar dossiers volledig digitaal behandelen. Poststukken met de 
vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan 
de geadresseerde bezorgd./

www.inbo.be 

///
To call in the statistician after the experiment is done may be no 
more than asking him to perform a post-mortem examination: he may be 
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does 
not ensure that a reasonable answer can be extracted from a given 
body of data. ~ John Tukey

///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker >:


    Thank you! (I know about package_dependencies() but ran into
    precisely the same problem and didn't want to re-implement it ...)

    On 2024-04-18 9:11 a.m., Josiah Parry wrote:
 > Well, after trying to install the package, I believe the issue is
 > because margins has been archived.
 >
 > https://cran.r-project.org/web/packages/margins/index.html
    
 > >
 >
 > You can check recursive dependencies using
 > `tools::package_dependencies("pkg", recursive = TRUE)` which
    would help
 > you in this case. I couldn't run it since the package is not
    available
 > on CRAN, however.
 >
 >
 > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker mailto:bbol...@gmail.com>
 > >> wrote:
 >
 >         The 'dotwhisker' package was archived on CRAN: from
 > https://cran.r-project.org/web/packages/dotwhisker/index.html
    
 >  >
 >
 >           Package ‘dotwhisker’ was removed from the CRAN 
repository

 >           ...
 >
 >           Archived on 2024-04-12 as requires archived package
    'prediction'.
 >
 >          However, I can't for the life of me see where this
    dependence
 >     could
 >     come from. Neither the DESCRIPTION file of the last-archived
    version on
 >     CRAN
 > 
  >>,

 >     nor the version on github
    
 >     >>, seem to
 >     show any signs of importing prediction ... ?? I suppose 
there's a

 >     possibility of a recursive dependence, but in that ca

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Ben Bolker 




On 2024-04-18 9:41 a.m., Uwe Ligges wrote:



On 18.04.2024 15:35, Ben Bolker wrote:
    Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN 
has apparently just caught up to checking.  What's a little 
frustrating (to me) is that the dependence of prediction on ffbase is 
*very* soft ("enhances") ...


No, but CRAN  has still not received an update and asked for this each 
month this year, so in Jan, Feb, and March without a response, so we 
assume prediction is unmaintained. Also, this was escalated to reverse 
depends.


Best,
Uwe Ligges


  Fair enough.  I'm not sure what the last sentence ("this was 
escalated to reverse depends") means though ...


  FWIW I did get an e-mail response from the maintainer two days ago 
suggesting that they were preparing a resubmission ...







On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
The cascade is even longer. prediction got archived because ffbase 
was no longer available. 
https://cran.r-project.org/web/packages/ffbase/ 



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR 
NATURE AND FOREST

Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be 
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
/Poststukken die naar dit adres worden gestuurd, worden ingescand en 
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid 
haar dossiers volledig digitaal behandelen. Poststukken met de 
vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan 
de geadresseerde bezorgd./

www.inbo.be 

///
To call in the statistician after the experiment is done may be no 
more than asking him to perform a post-mortem examination: he may be 
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does 
not ensure that a reasonable answer can be extracted from a given 
body of data. ~ John Tukey

///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker >:


    Thank you! (I know about package_dependencies() but ran into
    precisely the same problem and didn't want to re-implement it ...)

    On 2024-04-18 9:11 a.m., Josiah Parry wrote:
 > Well, after trying to install the package, I believe the issue is
 > because margins has been archived.
 >
 > https://cran.r-project.org/web/packages/margins/index.html
    
 > >
 >
 > You can check recursive dependencies using
 > `tools::package_dependencies("pkg", recursive = TRUE)` which
    would help
 > you in this case. I couldn't run it since the package is not
    available
 > on CRAN, however.
 >
 >
 > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker mailto:bbol...@gmail.com>
 > >> wrote:
 >
 >         The 'dotwhisker' package was archived on CRAN: from
 > https://cran.r-project.org/web/packages/dotwhisker/index.html
    
 >  >
 >
 >           Package ‘dotwhisker’ was removed from the CRAN 
repository

 >           ...
 >
 >           Archived on 2024-04-12 as requires archived package
    'prediction'.
 >
 >          However, I can't for the life of me see where this
    dependence
 >     could
 >     come from. Neither the DESCRIPTION file of the last-archived
    version on
 >     CRAN
 > 
  >>,

 >     nor the version on github
    
 >     >>, seem to
 >     show any signs of importing prediction ... ?? I suppose 
there's a

 >     possibility of a recursive dependence, but in that case why
    wouldn't
 >     the
 >     di

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Ben Bolker 

 To clarify, from an off-list conversation:

  AFAICT the chain is

  dotwhisker Imports
 margins, which Imports
   prediction, which Enhances
 ffbase  (archived in 2022 for 'coercion to logical' problems)

 (that conversation also pointed out that Enhances is a dependency *in 
the opposite direction* -- i.e. if A Enhances B, it's not entirely clear 
why the disappearance of B should matter at all ...)




On 2024-04-18 9:35 a.m., Ben Bolker wrote:
    Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN 
has apparently just caught up to checking.  What's a little frustrating 
(to me) is that the dependence of prediction on ffbase is *very* soft 
("enhances") ...


On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
The cascade is even longer. prediction got archived because ffbase was 
no longer available. https://cran.r-project.org/web/packages/ffbase/ 



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE 
AND FOREST

Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be 
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
/Poststukken die naar dit adres worden gestuurd, worden ingescand en 
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar 
dossiers volledig digitaal behandelen. Poststukken met de vermelding 
‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de 
geadresseerde bezorgd./

www.inbo.be 

///
To call in the statistician after the experiment is done may be no 
more than asking him to perform a post-mortem examination: he may be 
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does 
not ensure that a reasonable answer can be extracted from a given body 
of data. ~ John Tukey

///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker >:


    Thank you! (I know about package_dependencies() but ran into
    precisely the same problem and didn't want to re-implement it ...)

    On 2024-04-18 9:11 a.m., Josiah Parry wrote:
 > Well, after trying to install the package, I believe the issue is
 > because margins has been archived.
 >
 > https://cran.r-project.org/web/packages/margins/index.html
    
 > >
 >
 > You can check recursive dependencies using
 > `tools::package_dependencies("pkg", recursive = TRUE)` which
    would help
 > you in this case. I couldn't run it since the package is not
    available
 > on CRAN, however.
 >
 >
 > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker mailto:bbol...@gmail.com>
 > >> wrote:
 >
 >         The 'dotwhisker' package was archived on CRAN: from
 > https://cran.r-project.org/web/packages/dotwhisker/index.html
    
 >  
 >
 >
 >           Package ‘dotwhisker’ was removed from the CRAN 
repository

 >           ...
 >
 >           Archived on 2024-04-12 as requires archived package
    'prediction'.
 >
 >          However, I can't for the life of me see where this
    dependence
 >     could
 >     come from. Neither the DESCRIPTION file of the last-archived
    version on
 >     CRAN
 >  
  >>,

 >     nor the version on github
    
 >     >>, seem to
 >     show any signs of importing prediction ... ?? I suppose 
there's a

 >     possibility of a recursive dependence, but in that case why
    wouldn't
 >     the
 >     direct dependence be reported?
 >
 >     Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
 > 

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Uwe Ligges 



On 18.04.2024 15:35, Ben Bolker wrote:
    Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN 
has apparently just caught up to checking.  What's a little frustrating 
(to me) is that the dependence of prediction on ffbase is *very* soft 
("enhances") ...


No, but CRAN  has still not received an update and asked for this each 
month this year, so in Jan, Feb, and March without a response, so we 
assume prediction is unmaintained. Also, this was escalated to reverse 
depends.


Best,
Uwe Ligges




On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
The cascade is even longer. prediction got archived because ffbase was 
no longer available. https://cran.r-project.org/web/packages/ffbase/ 



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE 
AND FOREST

Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be 
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
/Poststukken die naar dit adres worden gestuurd, worden ingescand en 
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar 
dossiers volledig digitaal behandelen. Poststukken met de vermelding 
‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de 
geadresseerde bezorgd./

www.inbo.be 

///
To call in the statistician after the experiment is done may be no 
more than asking him to perform a post-mortem examination: he may be 
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does 
not ensure that a reasonable answer can be extracted from a given body 
of data. ~ John Tukey

///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker >:


    Thank you! (I know about package_dependencies() but ran into
    precisely the same problem and didn't want to re-implement it ...)

    On 2024-04-18 9:11 a.m., Josiah Parry wrote:
 > Well, after trying to install the package, I believe the issue is
 > because margins has been archived.
 >
 > https://cran.r-project.org/web/packages/margins/index.html
    
 > >
 >
 > You can check recursive dependencies using
 > `tools::package_dependencies("pkg", recursive = TRUE)` which
    would help
 > you in this case. I couldn't run it since the package is not
    available
 > on CRAN, however.
 >
 >
 > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker mailto:bbol...@gmail.com>
 > >> wrote:
 >
 >         The 'dotwhisker' package was archived on CRAN: from
 > https://cran.r-project.org/web/packages/dotwhisker/index.html
    
 >  
 >
 >
 >           Package ‘dotwhisker’ was removed from the CRAN 
repository

 >           ...
 >
 >           Archived on 2024-04-12 as requires archived package
    'prediction'.
 >
 >          However, I can't for the life of me see where this
    dependence
 >     could
 >     come from. Neither the DESCRIPTION file of the last-archived
    version on
 >     CRAN
 >  
  >>,

 >     nor the version on github
    
 >     >>, seem to
 >     show any signs of importing prediction ... ?? I suppose 
there's a

 >     possibility of a recursive dependence, but in that case why
    wouldn't
 >     the
 >     direct dependence be reported?
 >
 >     Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
 >     Imports: grid, gtable, gridExtra, stats, parameters, 
performance,

 >               patchwork, margins, dplyr, stringr, ggstance,
    rlang, purrr
 >     Suggests: ordina

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Ben Bolker 
   Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN 
has apparently just caught up to checking.  What's a little frustrating 
(to me) is that the dependence of prediction on ffbase is *very* soft 
("enhances") ...


On 2024-04-18 9:28 a.m., Thierry Onkelinx wrote:
The cascade is even longer. prediction got archived because ffbase was 
no longer available. https://cran.r-project.org/web/packages/ffbase/ 



ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE 
AND FOREST

Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be 
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
/Poststukken die naar dit adres worden gestuurd, worden ingescand en 
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar 
dossiers volledig digitaal behandelen. Poststukken met de vermelding 
‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de 
geadresseerde bezorgd./

www.inbo.be 

///
To call in the statistician after the experiment is done may be no more 
than asking him to perform a post-mortem examination: he may be able to 
say what the experiment died of. ~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not 
ensure that a reasonable answer can be extracted from a given body of 
data. ~ John Tukey

///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker >:


    Thank you! (I know about package_dependencies() but ran into
precisely the same problem and didn't want to re-implement it ...)

On 2024-04-18 9:11 a.m., Josiah Parry wrote:
 > Well, after trying to install the package, I believe the issue is
 > because margins has been archived.
 >
 > https://cran.r-project.org/web/packages/margins/index.html

 > >
 >
 > You can check recursive dependencies using
 > `tools::package_dependencies("pkg", recursive = TRUE)` which
would help
 > you in this case. I couldn't run it since the package is not
available
 > on CRAN, however.
 >
 >
 > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker mailto:bbol...@gmail.com>
 > >> wrote:
 >
 >         The 'dotwhisker' package was archived on CRAN: from
 > https://cran.r-project.org/web/packages/dotwhisker/index.html

 >   
  >
 >
 >           Package ‘dotwhisker’ was removed from the CRAN repository
 >           ...
 >
 >           Archived on 2024-04-12 as requires archived package
'prediction'.
 >
 >          However, I can't for the life of me see where this
dependence
 >     could
 >     come from. Neither the DESCRIPTION file of the last-archived
version on
 >     CRAN
 >   
   >>,

 >     nor the version on github

 >     >>, seem to
 >     show any signs of importing prediction ... ?? I suppose there's a
 >     possibility of a recursive dependence, but in that case why
wouldn't
 >     the
 >     direct dependence be reported?
 >
 >     Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
 >     Imports: grid, gtable, gridExtra, stats, parameters, performance,
 >               patchwork, margins, dplyr, stringr, ggstance,
rlang, purrr
 >     Suggests: ordinal, tibble, knitr, rmarkdown, broom
 >
 >         What am I missing?
 >
 >         (I'm concerned because I have packages that Suggest:
dotwhisker,
 >     and
 >     the absence of the package from repos is breaking GitHub Actions
 >     checks ...)
 >

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Thierry Onkelinx 
The cascade is even longer. prediction got archived because ffbase was no
longer available. https://cran.r-project.org/web/packages/ffbase/

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
*Postadres:* Koning Albert II-laan 15 bus 186, 1210 Brussel
*Poststukken die naar dit adres worden gestuurd, worden ingescand en
digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar
dossiers volledig digitaal behandelen. Poststukken met de vermelding
‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde
bezorgd.*
www.inbo.be

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///




Op do 18 apr 2024 om 15:25 schreef Ben Bolker :

>Thank you! (I know about package_dependencies() but ran into
> precisely the same problem and didn't want to re-implement it ...)
>
> On 2024-04-18 9:11 a.m., Josiah Parry wrote:
> > Well, after trying to install the package, I believe the issue is
> > because margins has been archived.
> >
> > https://cran.r-project.org/web/packages/margins/index.html
> > 
> >
> > You can check recursive dependencies using
> > `tools::package_dependencies("pkg", recursive = TRUE)` which would help
> > you in this case. I couldn't run it since the package is not available
> > on CRAN, however.
> >
> >
> > On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker  > > wrote:
> >
> > The 'dotwhisker' package was archived on CRAN: from
> > https://cran.r-project.org/web/packages/dotwhisker/index.html
> > 
> >
> >   Package ‘dotwhisker’ was removed from the CRAN repository
> >   ...
> >
> >   Archived on 2024-04-12 as requires archived package
> 'prediction'.
> >
> >  However, I can't for the life of me see where this dependence
> > could
> > come from. Neither the DESCRIPTION file of the last-archived version
> on
> > CRAN
> > <
> https://cran.r-project.org/src/contrib/Archive/dotwhisker/dotwhisker_0.8.1.tar.gz
> <
> https://cran.r-project.org/src/contrib/Archive/dotwhisker/dotwhisker_0.8.1.tar.gz
> >>,
> > nor the version on github  > >, seem to
> > show any signs of importing prediction ... ?? I suppose there's a
> > possibility of a recursive dependence, but in that case why wouldn't
> > the
> > direct dependence be reported?
> >
> > Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
> > Imports: grid, gtable, gridExtra, stats, parameters, performance,
> >   patchwork, margins, dplyr, stringr, ggstance, rlang, purrr
> > Suggests: ordinal, tibble, knitr, rmarkdown, broom
> >
> > What am I missing?
> >
> > (I'm concerned because I have packages that Suggest: dotwhisker,
> > and
> > the absence of the package from repos is breaking GitHub Actions
> > checks ...)
> >
> >
> > (This is cross-posted from an issue on the dotwhisker GH
> > repository:
> > https://github.com/fsolt/dotwhisker/issues/115
> > )
> >
> > __
> > R-package-devel@r-project.org 
> > mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > 
> >
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> (Acting) Graduate chair, Mathematics & Statistics
>  > E-mail is sent at my convenience; I don't expect replies outside of
> working hours.
>
> __
> 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] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Ben Bolker 
  Thank you! (I know about package_dependencies() but ran into 
precisely the same problem and didn't want to re-implement it ...)


On 2024-04-18 9:11 a.m., Josiah Parry wrote:
Well, after trying to install the package, I believe the issue is 
because margins has been archived.


https://cran.r-project.org/web/packages/margins/index.html 



You can check recursive dependencies using 
`tools::package_dependencies("pkg", recursive = TRUE)` which would help 
you in this case. I couldn't run it since the package is not available 
on CRAN, however.



On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker > wrote:


    The 'dotwhisker' package was archived on CRAN: from
https://cran.r-project.org/web/packages/dotwhisker/index.html


      Package ‘dotwhisker’ was removed from the CRAN repository
      ...

      Archived on 2024-04-12 as requires archived package 'prediction'.

     However, I can't for the life of me see where this dependence
could
come from. Neither the DESCRIPTION file of the last-archived version on
CRAN
>,
nor the version on github >, seem to
show any signs of importing prediction ... ?? I suppose there's a
possibility of a recursive dependence, but in that case why wouldn't
the
direct dependence be reported?

Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
Imports: grid, gtable, gridExtra, stats, parameters, performance,
          patchwork, margins, dplyr, stringr, ggstance, rlang, purrr
Suggests: ordinal, tibble, knitr, rmarkdown, broom

    What am I missing?

    (I'm concerned because I have packages that Suggest: dotwhisker,
and
the absence of the package from repos is breaking GitHub Actions
checks ...)


    (This is cross-posted from an issue on the dotwhisker GH
repository:
https://github.com/fsolt/dotwhisker/issues/115
)

__
R-package-devel@r-project.org 
mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel




--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of 
working hours.


__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Josiah Parry 
Well, after trying to install the package, I believe the issue is because
margins has been archived.

https://cran.r-project.org/web/packages/margins/index.html

You can check recursive dependencies using
`tools::package_dependencies("pkg", recursive = TRUE)` which would help you
in this case. I couldn't run it since the package is not available on CRAN,
however.


On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker  wrote:

>The 'dotwhisker' package was archived on CRAN: from
> https://cran.r-project.org/web/packages/dotwhisker/index.html
>
>  Package ‘dotwhisker’ was removed from the CRAN repository
>  ...
>
>  Archived on 2024-04-12 as requires archived package 'prediction'.
>
> However, I can't for the life of me see where this dependence could
> come from. Neither the DESCRIPTION file of the last-archived version on
> CRAN
> <
> https://cran.r-project.org/src/contrib/Archive/dotwhisker/dotwhisker_0.8.1.tar.gz>,
>
> nor the version on github , seem to
> show any signs of importing prediction ... ?? I suppose there's a
> possibility of a recursive dependence, but in that case why wouldn't the
> direct dependence be reported?
>
> Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
> Imports: grid, gtable, gridExtra, stats, parameters, performance,
>  patchwork, margins, dplyr, stringr, ggstance, rlang, purrr
> Suggests: ordinal, tibble, knitr, rmarkdown, broom
>
>What am I missing?
>
>(I'm concerned because I have packages that Suggest: dotwhisker, and
> the absence of the package from repos is breaking GitHub Actions checks
> ...)
>
>
>(This is cross-posted from an issue on the dotwhisker GH repository:
> https://github.com/fsolt/dotwhisker/issues/115)
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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[R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

2024-04-18 Thread Ben Bolker 
  The 'dotwhisker' package was archived on CRAN: from 
https://cran.r-project.org/web/packages/dotwhisker/index.html


Package ‘dotwhisker’ was removed from the CRAN repository
...

Archived on 2024-04-12 as requires archived package 'prediction'.

   However, I can't for the life of me see where this dependence could 
come from. Neither the DESCRIPTION file of the last-archived version on 
CRAN 
, 
nor the version on github , seem to 
show any signs of importing prediction ... ?? I suppose there's a 
possibility of a recursive dependence, but in that case why wouldn't the 
direct dependence be reported?


Depends: R (>= 3.2.0), ggplot2 (>= 2.2.1),
Imports: grid, gtable, gridExtra, stats, parameters, performance,
patchwork, margins, dplyr, stringr, ggstance, rlang, purrr
Suggests: ordinal, tibble, knitr, rmarkdown, broom

  What am I missing?

  (I'm concerned because I have packages that Suggest: dotwhisker, and 
the absence of the package from repos is breaking GitHub Actions checks ...)



  (This is cross-posted from an issue on the dotwhisker GH repository: 
https://github.com/fsolt/dotwhisker/issues/115)


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