[R] roxygen2 v6.0.0

[Bert Gunter]

Marc:

You miss Yihui's point I think: roxygen2 will generate the (Namespace
and other) files for you. See its documentation for how (the
directives to put in your comments).

-- Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Feb 6, 2017 at 9:38 AM, Marc Girondot via R-help
<r-help at r-project.org> wrote:
> Le 06/02/2017 à 17:14, Yihui Xie a écrit :
>>
>> If your package source is version controlled (meaning you are free to
>> regret any time), I'd recommend you to delete the three files
>> NAMESPACE, chr.Rd, and essai-package.Rd. Then try to roxygenize again.
>> Basically the warnings you saw indicates that roxygen2 failed to find
>> the line
>>
>> % Generated by roxygen2: do not edit by hand
>>
>> in your NAMESPACE and .Rd files, so it thinks these files were
>> probably not previously generated by roxygen2. I think the cause is
>> package.skeleton(), which generated the Rd files. Seriously, friends
>> don't let friends use package.skeleton()... (it is 2017 now)
>
> Thanks ! It works perfectly after removing the /man/ folder and the
> NAMESPACE file.
> I didn't know that package.skeleton() was out-of-age !
> That's true that it is easy to generate the skeleton manually.
>
> Marc
>>
>>
>> Regards,
>> Yihui
>> --
>> Yihui Xie <xieyihui at gmail.com>
>> Web: http://yihui.name
>>
>>
>> On Mon, Feb 6, 2017 at 9:46 AM, Marc Girondot via R-help
>> <r-help at r-project.org> wrote:
>>>
>>> Hi,
>>>
>>> I used roxygen2 v5.0.1 to document my package, and all was ok. I have
>>> just
>>> updated to roxygen2 v6.0.0 and my script is broken and I can't find why.
>>>
>>> I have done a simple version of a package folder as a test with 3 files:
>>> chr.R, essai-package.R and DESCRIPTION.
>>>
>>> Previously, I did:
>>>
>>> package.skeleton("essai",code_files=c('chr.R',"essai-package.R"))
>>> roxygenize("essai")
>>> system(paste0("R CMD build '", getwd(), "/essai'"))
>>> install.packages(file.path(getwd(), "essai_1.0.tar.gz"), repos = NULL,
>>> type="source")
>>>
>>> And it worked well.
>>>
>>> Now I get an error at the second line: roxygenize("essai")
>>>
>>>> roxygenize("essai")
>>>
>>> First time using roxygen2. Upgrading automatically...
>>> Updating roxygen version in
>>>
>>> /Users/marcgirondot/Documents/Espace_de_travail_R/Package_Essai/essai/DESCRIPTION
>>> Warning: The existing 'NAMESPACE' file was not generated by roxygen2, and
>>> will not be overwritten.
>>> Warning: The existing 'chr.Rd' file was not generated by roxygen2, and
>>> will
>>> not be overwritten.
>>> Warning: The existing 'essai-package.Rd' file was not generated by
>>> roxygen2,
>>> and will not be overwritten.
>>>
>>> And of course it fails after.
>>>
>>> Are you aware of this situation ? And do you have a solution ?
>>>
>>> Thanks a lot
>>>
>>> Marc
>>>
>>>
>>> A file DESCRIPTION:
>>>
>>> Package: essai
>>> Type: Package
>>> Title: Package Used For Try
>>> Version: 1.0
>>> Date: 2017-02-06
>>> Author: Marc Girondot <marc.girondot at u-psud.fr>
>>> Maintainer: Marc Girondot <marc.girondot at u-psud.fr>
>>> Description: Trying package.
>>> Depends: R (>= 2.14.2)
>>> License: GPL-2
>>> LazyData: yes
>>> LazyLoad: yes
>>> Encoding: UTF-8
>>> RoxygenNote: 6.0.0
>>>
>>> A file essai-package.R (essai=try in French):
>>>
>>> #' Trying package
>>> #'
>>> #' \tabular{ll}{
>>> #'  Package: \tab essai\cr
>>> #'  Type: \tab Package\cr
>>> #'  Version: \tab 1.0 - build 1\cr
>>> #'  Date: \tab 2017-02-06\cr
>>> #'  License: \tab GPL (>= 2)\cr
>>> #'  LazyLoad: \tab yes\cr
>>> #'  }
>>> #' @title The package essai
>>> #' @author Marc Girondot \email{marc.girondot@@u-psud.fr}
>>> #' @docType package
>>> #' @name essai-package
>>>
>>> NULL
>>>
>>> A file chr.R:
>>>
>>> #' chr returns the characters defined by the codes
>>> #' @title Return the characters defined by the codes
>>> #' @author Based on this blog:
>>> http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html
>>> #' @return A string with characters defined by the codes
>>> #' @param n The vector with codes
>>> #' @description Return a string with characters defined by the codes.
>>> J'essaye avec un code utf-8: ê.
>>> #' @examples
>>> #' chr(65:75)
>>> #' chr(unlist(tapply(144:175, 144:175, function(x) {c(208, x)})))
>>> #' @encoding UTF-8
>>> #' @export
>>>
>>>
>>> chr <- function(n) {
>>>      rawToChar(as.raw(n))
>>>      }
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.