[R-pkg-devel] package docu
On 27/01/2019 2:49 a.m., Troels Ring wrote:
Thanks a lot - I followed your suggestion, and prompt generated under usage: data(kw) - which is not working as kw is just a single number. So I just removed the usage section and no complaints are left. Thanks for all help!
Sorry, I misread an earlier message and thought that kw was a function, not data. If it is data, use promptData() instead of prompt. Duncan Murdoch
BW Troels -----Oprindelig meddelelse----- Fra: Duncan Murdoch <murdoch.duncan at gmail.com> Sendt: 26. januar 2019 22:08 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: SV: [R-pkg-devel] package docu 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 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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