[R-pkg-devel] problems documenting data sets

It's hard to be sure without seeing your package, but it *sounds* as 
though you have a data set "Brom" (in <package>/data ?) but you have 
*documented* a data set named "brom".  So you should either change the 
name of the data set to "brom" or change your help file to document "Brom".

It is of course entirely possible that I am misunderstanding what is 
going on, in which case I apologise for the noise.

cheers,

Rolf

Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

On 1/19/19 11:46 PM, Troels Ring wrote:
> Dear friends ? I still get some warning although the package runs just fine.
> 
> checking for missing documentation entries ... WARNING
> 
>    Undocumented data sets:
> 
>      'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
> 
>      'Brom' 'pHOBS'
> 
>    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
> 
> K?rsel stoppet (run stopped)
> 
>   
> 
> But the only place I have  any mentions of brom is here below and in no place I have capital Brom. So what should I make of this?
> 
>   
> 
> \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{WA}{List of buffers with list of dissociation constants.}
> 
>    }
> 
> }
> 
> \source{
> 
> Glaser RE et al. Dynamical approach to multiequilibriia problems for mixtures of
> 
> acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
> 
> }
> 
> \examples{
> 
> data(brom)
> 
> ## maybe str(brom) ; plot(brom) ...
> 
> }
> 
> \keyword{datasets}

I was first thinking there could be an occurence of Brom with a capital B in the package somewhere.
In which case you could run from the current package main directory:

cat("All files in R folder\n", file="AllFiles.R")
for(f in dir("R",full=T)) cat(readLines(f), file="AllFiles.R", sep="\n", append=TRUE)

and search for Brom in that file...
But Rolf is likely right. I was thinking the wrong way around...

Berry

Dear friends ? I still get some warning although the package runs just fine.

checking for missing documentation entries ... WARNING

  Undocumented data sets:

    'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'

    'Brom' 'pHOBS'

  All user-level objects in a package should have documentation entries.
[SNIP]

Thank you so much - I used the search in files function in RStudio and also looked everywhere as well as I could - but seemingly: no - everywhere only "brom". So since the functions runs as expected and I can make a workable binary package I guess I will just continue improving the functionalities and see if I eventually get a hunch

All best wishes
Troels 

-----Oprindelig meddelelse-----
Fra: Rolf Turner <r.turner at auckland.ac.nz> 
Sendt: 19. januar 2019 23:12
Til: Troels Ring <tring at gvdnet.dk>
Cc: package-develop <r-package-devel at r-project.org>
Emne: Re: [R-pkg-devel] problems documenting data sets


It's hard to be sure without seeing your package, but it *sounds* as though you have a data set "Brom" (in <package>/data ?) but you have
*documented* a data set named "brom".  So you should either change the name of the data set to "brom" or change your help file to document "Brom".

It is of course entirely possible that I am misunderstanding what is going on, in which case I apologise for the noise.

cheers,

Rolf

--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

Dear friends ? I still get some warning although the package runs just fine.

checking for missing documentation entries ... WARNING

   Undocumented data sets:

     'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'

     'Brom' 'pHOBS'

   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

K rsel stoppet (run stopped)

  

But the only place I have  any mentions of brom is here below and in no place I have capital Brom. So what should I make of this?

  

\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{WA}{List of buffers with list of dissociation constants.}

   }

}

\source{

Glaser RE et al. Dynamical approach to multiequilibriia problems for 
mixtures of

acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016

}

\examples{

data(brom)

## maybe str(brom) ; plot(brom) ...

}

\keyword{datasets}

Thanks a lot - I tried your script but it didn't turn up anything like Brom
but  in one place I had Bromic acid - which I changed to bromic acid to no
avail.

So I continue trying to find out what goes on

BW

Troels

 

Fra: Berry Boessenkool <berryboessenkool at hotmail.com> 
Sendt: 19. januar 2019 23:47
Til: Troels Ring <tring at gvdnet.dk>; R package devel
<r-package-devel at r-project.org>
Emne: Re: [R-pkg-devel] problems documenting data sets

 

 

I was first thinking there could be an occurence of Brom with a capital B in
the package somewhere.

In which case you could run from the current package main directory:

 

cat("All files in R folder\n", file="AllFiles.R")

for(f in dir("R",full=T)) cat(readLines(f), file="AllFiles.R", sep="\n",
append=TRUE)

 

and search for Brom in that file...

But Rolf is likely right. I was thinking the wrong way around...

 

Berry

 

  _____  

From: R-package-devel <r-package-devel-bounces at r-project.org
<mailto:r-package-devel-bounces at r-project.org> > on behalf of Troels Ring
<tring at gvdnet.dk <mailto:tring at gvdnet.dk> >
Sent: Saturday, January 19, 2019 11:46
To: package-develop
Subject: [R-pkg-devel] problems documenting data sets 

 

Dear friends - I still get some warning although the package runs just fine.

checking for missing documentation entries ... WARNING

  Undocumented data sets:

    'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'

    'Brom' 'pHOBS'

  All user-level objects in a package should have documentation entries.
[SNIP]

Did you mention where your package source can be downloaded from, e.g., github? Because obviously it is then much easier for people to help.

Martin Morgan

?On 1/20/19, 12:55 PM, "R-package-devel on behalf of Troels Ring" <r-package-devel-bounces at r-project.org on behalf of tring at gvdnet.dk> wrote:

    Thank you so much - I used the search in files function in RStudio and also looked everywhere as well as I could - but seemingly: no - everywhere only "brom". So since the functions runs as expected and I can make a workable binary package I guess I will just continue improving the functionalities and see if I eventually get a hunch
    
    All best wishes
    Troels 
    
    -----Oprindelig meddelelse-----
    Fra: Rolf Turner <r.turner at auckland.ac.nz> 
    Sendt: 19. januar 2019 23:12
    Til: Troels Ring <tring at gvdnet.dk>
    Cc: package-develop <r-package-devel at r-project.org>
    Emne: Re: [R-pkg-devel] problems documenting data sets
    
    
    It's hard to be sure without seeing your package, but it *sounds* as though you have a data set "Brom" (in <package>/data ?) but you have
    *documented* a data set named "brom".  So you should either change the name of the data set to "brom" or change your help file to document "Brom".
    
    It is of course entirely possible that I am misunderstanding what is going on, in which case I apologise for the noise.
    
    cheers,
    
    Rolf
    
    --
    Honorary Research Fellow
    Department of Statistics
    University of Auckland
    Phone: +64-9-373-7599 ext. 88276

> Dear friends ? I still get some warning although the package runs just fine.
    > 
    > checking for missing documentation entries ... WARNING
    > 
    >    Undocumented data sets:
    > 
    >      'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
    > 
    >      'Brom' 'pHOBS'
    > 
    >    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
    > 
    > K rsel stoppet (run stopped)
    > 
    >   
    > 
    > But the only place I have  any mentions of brom is here below and in no place I have capital Brom. So what should I make of this?
    > 
    >   
    > 
    > \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{WA}{List of buffers with list of dissociation constants.}
    > 
    >    }
    > 
    > }
    > 
    > \source{
    > 
    > Glaser RE et al. Dynamical approach to multiequilibriia problems for 
    > mixtures of
    > 
    > acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
    > 
    > }
    > 
    > \examples{
    > 
    > data(brom)
    > 
    > ## maybe str(brom) ; plot(brom) ...
    > 
    > }
    > 
    > \keyword{datasets}
    
    ______________________________________________
    R-package-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel

Thank you so much -  this is just the first package I've made so I didn't put it  out yet. Will follow your suggestion next time
BW
Troels

-----Oprindelig meddelelse-----
Fra: Martin Morgan <mtmorgan.bioc at gmail.com> 
Sendt: 20. januar 2019 19:14
Til: Troels Ring <tring at gvdnet.dk>; 'Rolf Turner' <r.turner at auckland.ac.nz>
Cc: 'package-develop' <r-package-devel at r-project.org>
Emne: Re: [R-pkg-devel] problems documenting data sets

Did you mention where your package source can be downloaded from, e.g., github? Because obviously it is then much easier for people to help.

Martin Morgan

?On 1/20/19, 12:55 PM, "R-package-devel on behalf of Troels Ring" <r-package-devel-bounces at r-project.org on behalf of tring at gvdnet.dk> wrote:

    Thank you so much - I used the search in files function in RStudio and also looked everywhere as well as I could - but seemingly: no - everywhere only "brom". So since the functions runs as expected and I can make a workable binary package I guess I will just continue improving the functionalities and see if I eventually get a hunch
    
    All best wishes
    Troels 
    
    -----Oprindelig meddelelse-----
    Fra: Rolf Turner <r.turner at auckland.ac.nz> 
    Sendt: 19. januar 2019 23:12
    Til: Troels Ring <tring at gvdnet.dk>
    Cc: package-develop <r-package-devel at r-project.org>
    Emne: Re: [R-pkg-devel] problems documenting data sets
    
    
    It's hard to be sure without seeing your package, but it *sounds* as though you have a data set "Brom" (in <package>/data ?) but you have
    *documented* a data set named "brom".  So you should either change the name of the data set to "brom" or change your help file to document "Brom".
    
    It is of course entirely possible that I am misunderstanding what is going on, in which case I apologise for the noise.
    
    cheers,
    
    Rolf
    
    --
    Honorary Research Fellow
    Department of Statistics
    University of Auckland
    Phone: +64-9-373-7599 ext. 88276

> Dear friends ? I still get some warning although the package runs just fine.
    > 
    > checking for missing documentation entries ... WARNING
    > 
    >    Undocumented data sets:
    > 
    >      'Cl' 'K' 'Na' 'TOTAL' 'WA' 'INPUT' 'Alb' 'Ca' 'Lact' 'Mg' 'PCO2' 'S1'
    > 
    >      'Brom' 'pHOBS'
    > 
    >    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
    > 
    > K rsel stoppet (run stopped)
    > 
    >   
    > 
    > But the only place I have  any mentions of brom is here below and in no place I have capital Brom. So what should I make of this?
    > 
    >   
    > 
    > \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{WA}{List of buffers with list of dissociation constants.}
    > 
    >    }
    > 
    > }
    > 
    > \source{
    > 
    > Glaser RE et al. Dynamical approach to multiequilibriia problems for 
    > mixtures of
    > 
    > acids and their conjugate bases. J Chem Educ 2014; 91: 1009-1016
    > 
    > }
    > 
    > \examples{
    > 
    > data(brom)
    > 
    > ## maybe str(brom) ; plot(brom) ...
    > 
    > }
    > 
    > \keyword{datasets}
    
    ______________________________________________
    R-package-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel