[R-pkg-devel] package docu

[Duncan Murdoch]

On 26/01/2019 9:04 a.m., Troels Ring wrote:
> Thanks a lot - I tried with prompt(kw) and that warning disappeared but instead I got another
>> checking for code/documentation mismatches ... WARNING
>    Data with usage in documentation object 'kw' but not in code:
>      Kw
> 
> And the code is really full og kw -

That message is about the Rd file, not the code.  Look for Kw in the 
\usage section.

You haven't pushed this file to Github, so I can't offer any more advice.

Duncan Murdoch

> 
> I'm so sorry to bother
> BW
> Troels
> 
> -----Oprindelig meddelelse-----
> Fra: Duncan Murdoch <murdoch.duncan using gmail.com>
> Sendt: 26. januar 2019 14:45
> Til: Troels Ring <tring using gvdnet.dk>; 'Michael Dewey' <lists using dewey.myzen.co.uk>; 'package-develop' <r-package-devel using r-project.org>
> Emne: Re: [R-pkg-devel] package docu
> 
> On 26/01/2019 8:31 a.m., Troels Ring wrote:
>> Dear Michael - fantastic: TOTAL is now acknowledged -- so I only need the constants kw, K3, and Kc from the utility_acid.r file - how for format their documentation - they are available as required inside and outside the package.
> 
> Within R, set your working directory to the man directory for your package, then run
> 
>     prompt(kw)
> 
> and it will create kw.Rd in the right format.  You just need to edit it to fill in the details.  There will be comments in the file explaining what to do.  Don't put quotes on the name; prompt("kw") is wrong.
> 
> Duncan Murdoch
> 
> 
>>
>> All best wishes
>> Troels
>>
>> -----Oprindelig meddelelse-----
>> Fra: Michael Dewey <lists using dewey.myzen.co.uk>
>> Sendt: 26. januar 2019 13:17
>> Til: Troels Ring <tring using gvdnet.dk>; package-develop
>> <r-package-devel using r-project.org>
>> Emne: Re: [R-pkg-devel] package docu
>>
>> Dear Troels
>>
>> What happens if you add \alias{TOTAL}
>>
>> Michael
>>
>> On 26/01/2019 08:15, Troels Ring wrote:
>>> Dear friends - I'm struggling to get the documentation of my package
>>> correct. The working package is now (with your help!) at
>>>
>>> devtools::install_github("troelsring/ABCharge")
>>>
>>> and in its proto version includes only a single dataset "brom.RData"
>>> which has two components, a data.frame "brom" and a matrix TOTAL.
>>> These are documented in the brom.RD file shown below.
>>>
>>>     
>>>
>>>     
>>>
>>> \name{brom}
>>>
>>> \alias{brom}
>>>
>>> \docType{data}
>>>
>>> \title{
>>>
>>> bromic acid data from Glaser et al 2014
>>>
>>> }
>>>
>>> \description{
>>>
>>>      Data to find optimal pK for bromic acid
>>>
>>> }
>>>
>>> \usage{data("brom")}
>>>
>>> \format{
>>>
>>> A workspace.
>>>
>>>      \describe{
>>>
>>>        \item{brom}{Dataframe of Table S4 in Glaser et al.}
>>>
>>>        \item{TOTAL}{Matrix of buffer concentrations.}
>>>
>>>      }
>>>
>>> }
>>>
>>> \source{
>>>
>>> Glaser RE et al. Dynamical approach to multiequilibria problems for
>>> mixtures of
>>>
>>> acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
>>>
>>> }
>>>
>>> \examples{
>>>
>>> data(brom)
>>>
>>> ----- a long example - works well
>>>
>>>     
>>>
>>> Now when running ctrl-shift-E, I get
>>>
>>>     
>>>
>>>> checking for missing documentation entries ... WARNING
>>>
>>>      Undocumented code objects:
>>>
>>>        'K3' 'Kc' 'kw'
>>>
>>>      Undocumented data sets:
>>>
>>>        'TOTAL'
>>>
>>>      All user-level objects in a package should have documentation entries.
>>>
>>>      See chapter 'Writing R documentation files' in the 'Writing R
>>>
>>>      Extensions' manual.
>>>
>>>     
>>>
>>> 0 errors v | 1 warning x | 0 notes v
>>>
>>> Fejl: R CMD check found WARNINGs
>>>
>>> run stoppet
>>>
>>>     
>>>
>>> Exited with status 1.
>>>
>>>     
>>>
>>> I wonder why the specification of TOTAL in the RD file is ignored?
>>>
>>>     
>>>
>>> Also the three constants kw, Kc, and K3 are not properly documented.
>>> They are declared and exported in the utility_acid.r file and I have
>>> tried to document them as  @params in that file but it seems to be
>>> ignored and cause other problems so I have them at present
>>> undocumented since I don't know where to put the documentation.
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
>> --
>> Michael
>> http://www.dewey.myzen.co.uk/home.html
>>
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
> 
>