[R-pkg-devel] package docu

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 -

I'm so sorry to bother
BW
Troels

-----Oprindelig meddelelse-----
Fra: Duncan Murdoch <murdoch.duncan at gmail.com>
Sendt: 26. januar 2019 14:45
Til: Troels Ring <tring at gvdnet.dk>; 'Michael Dewey' 
<lists at dewey.myzen.co.uk>; 'package-develop' 
<r-package-devel at 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 at dewey.myzen.co.uk>
Sendt: 26. januar 2019 13:17
Til: Troels Ring <tring at gvdnet.dk>; package-develop 
<r-package-devel at 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.


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--
Michael
http://www.dewey.myzen.co.uk/home.html