Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

2024-03-06 Thread Yohann Foucher
Dear all,

Thank you for your proposals and discussions. Accordingly, because it seems 
there is no relevant alternative, I decided to propose an update of the « 
survivalmodels » instead of the initial maintener for repositioning it in the 
main CRAN repository and avoid the archiving of my package.

Thanks again.

Yohann


> Le 5 mars 2024 à 22:25, Dirk Eddelbuettel  a écrit :
> 
> 
> On 5 March 2024 at 15:12, Duncan Murdoch wrote:
> | On 05/03/2024 2:26 p.m., Dirk Eddelbuettel wrote:
> | > The default behaviour is to build after every commit to the main branch.  
> But
> | > there are options. On the repo I mentioned we use
> | > 
> | >  "branch": "*release",
> | 
> | Where do you put that?  I don't see r2u on R-universe, so I guess you're 
> | talking about a different repo; which one?
> 
> In the (optional) control repo that can drive your 'r-universe', and the file
> has to be named 'packages.json'. For you the repo would
> 
>https://github.com/dmurdoch/dmurdoch.r-universe.dev
> 
> (and the naming rule was tightened by Jeroen recently -- we used to call
> these just 'universe', now it has to match your runiverse)
> 
> The file packages.json would then have a block
> 
>  {
>"package": "rgl",
>"maintainer": "Duncan Murdoch "
>"url": "https://github.com/dmurdoch/rgl;,
>"available": true,
>"branch": "*release"
>  }
> 
> The reference I mentioned is our package 'tiledbsoma' (joint work of TileDB
> and CZI, in https://github.com/single-cell-data/TileDB-SOMA) and described 
> here:
> 
> https://github.com/TileDB-Inc/tiledb-inc.r-universe.dev/blob/master/packages.json
>  
> 
> (and you can ignore the '"subdir": "apis/r"' which is a facet local to that 
> repo).
> 
> Note that 'my' packages.json in my eddelbuettel.r-universe.dev ie
> 
> https://github.com/eddelbuettel/eddelbuettel.r-universe.dev/blob/master/packages.json
> 
> also describe but without the '"branch": "*release"' and that builds with 
> every merge to
> the main branch by my choice; that build is mine and 'inofficial' giving us 
> two.
> 
> | > It is under your control. You could document how to install via `remotes`
> | > from that branch.  As so often, it's about trading one thing off for 
> another.
> | 
> | I do that, but my documentation falls off the bottom of the screen, and 
> | the automatic docs generated by R-universe are at the top.
> 
> I always get lost in the r-universe docs too. Some, as Jeroen kindly reminded
> me the other day, are here:  https://github.com/r-universe-org
> 
> Dirk
> 
> -- 
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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[R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

2024-03-05 Thread Yohann Foucher
Dear R-Members,


I just have submitted an update of the ‘survivalSL' package because the last 
version depends on the ‘survivalmodels’ package, which has been recently 
archived.  In the DESCRIPTION file of the new version 0.93 of the ‘survivalSL' 
package, I've moved ‘survivalmodels' from "Depends" to the ‘Suggests'. I 
thought this would solve the problem. Indeed, the 'survivalSL’ package can 
function without the ‘survivalmodels’ package if the user does not include the 
related learner (survival neural network) in the learning ensemble. 
Nevertheless, the new version 0.93 was archived again. 

I’m working on the estimation of a survival neural network without the 
‘survivalmodels’ package but this developments will take a long time. During 
this period, do you have any idea to avoid the archiving of my package?

Thank you for your help.


Yohann

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[R-pkg-devel] Check: Rd \usage sections, Result: The \usage entries for S3 methods should use the \method markup and not their full name.

2023-03-22 Thread Yohann Foucher
Dear all,

I maintain the RISCA package and I have the following new issue when I submit 
the novel version 1.0.4 on the CRAN:

***
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
 Maintainer: 'Yohann Foucher mailto:yohann.fouc...@univ-poitiers.fr>>'

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: Rd \usage sections, Result: NOTE
 S3 methods shown with full name in documentation object 'nnet.time':
   'nnet.time'

 The \usage entries for S3 methods should use the \method markup and not
 their full name.
 See chapter 'Writing R documentation files' in the 'Writing R
 Extensions' manual.
***

Nevertheless, as for other S3 methods, I did not change this function compared 
to the last version 1.0.3 (which is online). I use the \method markup in the Rd 
file:

***
\usage{
\method{predict}{nnet.time}(object, ..., newdata, newtimes)
}
***

When I use «  R CMD check --as-cran », this NOTE is not identified. Do you have 
any idea of solution?

Thank you for your support.

Yohann


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