[R-pkg-devel] package docu
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package docu
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.
All best wishes
Troels
-Oprindelig meddelelse-
Fra: Michael Dewey
Sendt: 26. januar 2019 13:17
Til: Troels Ring ; package-develop
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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
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
Sendt: 26. januar 2019 13:17
Til: Troels Ring ; package-develop
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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [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
Sendt: 26. januar 2019 14:45
Til: Troels Ring ; 'Michael Dewey' ;
'package-develop'
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
> Sendt: 26. januar 2019 13:17
> Til: Troels Ring ; package-develop
>
> 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@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package docu
Well in the usage section it says Kw but elsewhere kw so you need to
make them match. Probably some "helpful" part of your system is
capitalising things without you noticing.
Michael
On 26/01/2019 14:04, 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 -
I'm so sorry to bother
BW
Troels
-Oprindelig meddelelse-
Fra: Duncan Murdoch
Sendt: 26. januar 2019 14:45
Til: Troels Ring ; 'Michael Dewey' ;
'package-develop'
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
Sendt: 26. januar 2019 13:17
Til: Troels Ring ; package-develop
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@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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package docu
Thanks a lot - but it is really kw and not Kw everywhere - according to "find
in files" etc - thanks a lot for your patience and interest!
BW
Troels
-Oprindelig meddelelse-
Fra: Michael Dewey
Sendt: 26. januar 2019 15:48
Til: Troels Ring ; 'Duncan Murdoch'
; 'package-develop'
Emne: Re: SV: [R-pkg-devel] package docu
Well in the usage section it says Kw but elsewhere kw so you need to make them
match. Probably some "helpful" part of your system is capitalising things
without you noticing.
Michael
On 26/01/2019 14:04, 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 -
>
> I'm so sorry to bother
> BW
> Troels
>
> -Oprindelig meddelelse-
> Fra: Duncan Murdoch
> Sendt: 26. januar 2019 14:45
> Til: Troels Ring ; 'Michael Dewey'
> ; 'package-develop'
>
> 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
>> Sendt: 26. januar 2019 13:17
>> Til: Troels Ring ; package-develop
>>
>> 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@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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [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
Sendt: 26. januar 2019 14:45
Til: Troels Ring ; 'Michael Dewey' ;
'package-develop'
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
Sendt: 26. januar 2019 13:17
Til: Troels Ring ; package-develop
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]]
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--
Michael
http://www.dewey.myzen.co.uk/home.html
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Re: [R-pkg-devel] package docu
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!
BW
Troels
-Oprindelig meddelelse-
Fra: Duncan Murdoch
Sendt: 26. januar 2019 22:08
Til: Troels Ring ; 'Michael Dewey' ;
'package-develop'
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
> Sendt: 26. januar 2019 14:45
> Til: Troels Ring ; 'Michael Dewey'
> ; 'package-develop'
>
> 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
>> Sendt: 26. januar 2019 13:17
>> Til: Troels Ring ; package-develop
>>
>> 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@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@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
>
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