Re: [R-pkg-devel] Appropriate keyword in help file.

[Jeff Newmiller]

You can get away with a lot if you are not distributing your package. But I 
usually try to satisfy R CMD check at least.

On April 16, 2020 5:50:04 PM PDT, Rolf Turner  wrote:
>
>On 17/04/20 12:14 pm, Duncan Murdoch wrote:
>
>> On 16/04/2020 8:12 p.m., Rolf Turner wrote:
>>>
>>> I'm writing a package (just for my own use, for the time being at
>least)
>>> that contains a function for estimating the parameters of a
>>> distribution.  The function is essentially a wrapper for fitdistr()
>from
>>> the MASS package.
>>>
>>> When I looked at RShowDoc("KEYWORDS"), I could not find an
>appropriate
>>> keyword to use in the help file for this function.  There's "htest &
>>> Statistical Inference", but that's not right, since this function is
>>> about estimation, not hypothesis testing.  I'd hoped that there'd be
>a
>>> keyword "estimation" (or "point estimation") or something like that,
>but
>>> there isn't.
>>>
>>> I guess I can use "utilities" (???) or "misc", but these seem a bit
>>> unsatisfactory.
>>>
>>> Can anyone suggest a better idea?
>> 
>> Don't use any keyword. When was the last time you searched on one?
>
>
>I have *never* in my life searched on a keyword! :-)
>
>I just thought that it was an Immutable Law of the Universe that a help
>
>file had to have at least one keyword, and that the R Gods would rain 
>fire and brimstone down upon one's head if no keyword was supplied.
>
>In a similar vein:  would the R Gods allow me to make up my own keyword
>
>rather than choosing from those listed by RShowDoc("KEYWORDS")?
>
>Thanks.
>
>cheers,
>
>Rolf

-- 
Sent from my phone. Please excuse my brevity.

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Re: [R-pkg-devel] Appropriate keyword in help file.

[Rolf Turner]

On 17/04/20 12:14 pm, Duncan Murdoch wrote:


On 16/04/2020 8:12 p.m., Rolf Turner wrote:


I'm writing a package (just for my own use, for the time being at least)
that contains a function for estimating the parameters of a
distribution.  The function is essentially a wrapper for fitdistr() from
the MASS package.

When I looked at RShowDoc("KEYWORDS"), I could not find an appropriate
keyword to use in the help file for this function.  There's "htest &
Statistical Inference", but that's not right, since this function is
about estimation, not hypothesis testing.  I'd hoped that there'd be a
keyword "estimation" (or "point estimation") or something like that, but
there isn't.

I guess I can use "utilities" (???) or "misc", but these seem a bit
unsatisfactory.

Can anyone suggest a better idea?


Don't use any keyword. When was the last time you searched on one?



I have *never* in my life searched on a keyword! :-)

I just thought that it was an Immutable Law of the Universe that a help 
file had to have at least one keyword, and that the R Gods would rain 
fire and brimstone down upon one's head if no keyword was supplied.


In a similar vein:  would the R Gods allow me to make up my own keyword 
rather than choosing from those listed by RShowDoc("KEYWORDS")?


Thanks.

cheers,

Rolf

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

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Re: [R-pkg-devel] Appropriate keyword in help file.

[Duncan Murdoch]

On 16/04/2020 8:12 p.m., Rolf Turner wrote:


I'm writing a package (just for my own use, for the time being at least)
that contains a function for estimating the parameters of a
distribution.  The function is essentially a wrapper for fitdistr() from
the MASS package.

When I looked at RShowDoc("KEYWORDS"), I could not find an appropriate
keyword to use in the help file for this function.  There's "htest &
Statistical Inference", but that's not right, since this function is
about estimation, not hypothesis testing.  I'd hoped that there'd be a
keyword "estimation" (or "point estimation") or something like that, but
there isn't.

I guess I can use "utilities" (???) or "misc", but these seem a bit
unsatisfactory.

Can anyone suggest a better idea?


Don't use any keyword. When was the last time you searched on one?

Duncan Murdoch

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[R-pkg-devel] Appropriate keyword in help file.

[Rolf Turner]

I'm writing a package (just for my own use, for the time being at least)
that contains a function for estimating the parameters of a 
distribution.  The function is essentially a wrapper for fitdistr() from 
the MASS package.


When I looked at RShowDoc("KEYWORDS"), I could not find an appropriate 
keyword to use in the help file for this function.  There's "htest & 
Statistical Inference", but that's not right, since this function is 
about estimation, not hypothesis testing.  I'd hoped that there'd be a 
keyword "estimation" (or "point estimation") or something like that, but 
there isn't.


I guess I can use "utilities" (???) or "misc", but these seem a bit 
unsatisfactory.


Can anyone suggest a better idea?

cheers,

Rolf Turner

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

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Re: [R-pkg-devel] Detritus in temp directory - Note from submission of R package in CRAN

[Uwe Ligges]

On 16.04.2020 20:09, Duncan Murdoch wrote:

On 16/04/2020 1:11 p.m., David Andres Zamora Avila wrote:

  Hi,

I submitted my package in CRAN and always appearance the next NOTE.

Flavor: r-devel-linux-x86_64-debian-gcc
Check: for detritus in the temp directory, Result: NOTE
   Found the following files/directories:
 'RtmpcDoRWjr.nc'

I have tried to solve it in several ways (like if(interactive()), but 
I not

sure how can I solve it.


How was the file created?  What the check wants is that you delete it 
when you are finished with it.  You can use the unlink() function to do 
that.


Or better create it in tempdir(): I guess you used paste(tempdir(), ...) 
instead of file.path() and got afilename one level above tempdir()?


Best,
Uwe Ligges




Duncan Murdoch

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Re: [R-pkg-devel] Detritus in temp directory - Note from submission of R package in CRAN

[Duncan Murdoch]

On 16/04/2020 1:11 p.m., David Andres Zamora Avila wrote:

  Hi,

I submitted my package in CRAN and always appearance the next NOTE.

Flavor: r-devel-linux-x86_64-debian-gcc
Check: for detritus in the temp directory, Result: NOTE
   Found the following files/directories:
 'RtmpcDoRWjr.nc'

I have tried to solve it in several ways (like if(interactive()), but I not
sure how can I solve it.


How was the file created?  What the check wants is that you delete it 
when you are finished with it.  You can use the unlink() function to do 
that.


Duncan Murdoch

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[R-pkg-devel] Detritus in temp directory - Note from submission of R package in CRAN

[David Andres Zamora Avila]

 Hi,

I submitted my package in CRAN and always appearance the next NOTE.

Flavor: r-devel-linux-x86_64-debian-gcc
Check: for detritus in the temp directory, Result: NOTE
  Found the following files/directories:
'RtmpcDoRWjr.nc'

I have tried to solve it in several ways (like if(interactive()), but I not
sure how can I solve it.

Thanks.

Kind regards


-- 

David Zamora 
PhD Student, Universidad Nacional de Colombia, Bogotá
phone: +571 3165000 ext 13406
address: Av. NQS (Carrera 30) # 45-03, Hydraulics Lab (408-213)
email: dazamo...@unal.edu.co

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Re: [R-pkg-devel] Error vignette rebuilding and package imports when re-submitting package

[Fernando Roa]

Related thread:
https://stat.ethz.ch/pipermail/r-package-devel/2020q2/005300.html
best,

On Wed, Apr 15, 2020 at 9:13 AM Paul SAVARY 
wrote:

> Hello,
>
> I'm having trouble re-submitting a package (graph4lg).
>
> - With r-patched_osx, vignette rebuilding fails with the following message
> :
>
> checking re-building of vignette outputs ... [12s/16s] WARNING
> Error(s) in re-building vignettes:
> ...
> --- re-building ‘vignette_graph4lg.Rmd’ using rmarkdown
> dyld: lazy symbol binding failed: Symbol not found: chkstk_darwin
> Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X
> 10.15)
> Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: chkstk_darwin
> Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X
> 10.15)
> Expected in: /usr/lib/libSystem.B.dylib
>
> Error: processing vignette 'vignette_graph4lg.Rmd' failed with
> diagnostics:
> pandoc document conversion failed with error 6
> --- failed re-building ‘vignette_graph4lg.Rmd’
>
> SUMMARY: processing the following file failed:
> ‘vignette_graph4lg.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> - Besides, although I removed some unused packages from the imports in
> DESCRIPTION file, I still obtain this message :
>
> checking dependencies in R code ... NOTE
> Namespaces in Imports field not imported from:
> ‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’
> All declared Imports should be used.
>
> Except Rdpack which is needed to build the vignette, I removed these
> packages.
>
> Finally, although I submit version 0.4.0, I receive checking errors
> relative to version 0.3.0.
>
> I thank you in advance for your feedbacks.
> Regards
> Paul Savary
>
>
>
>
>
>
>
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>
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-- 
Fernando Roa

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Re: [R-pkg-devel] Error vignette rebuilding and package imports when re-submitting package

[Georgi Boshnakov]

Just add 

importFrom(Rdpack,  reprompt) 

in the NAMESPACE file (any function from Rdpack will do). 

Georgi Boshnakov

-Original Message-
From: R-package-devel  On Behalf Of Paul 
SAVARY
Sent: 15 April 2020 10:15
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] Error vignette rebuilding and package imports when 
re-submitting package

Hello, 

I'm having trouble re-submitting a package (graph4lg). 

- With r-patched_osx, vignette rebuilding fails with the following message : 

checking re-building of vignette outputs ... [12s/16s] WARNING
Error(s) in re-building vignettes: 
... 
--- re-building ‘vignette_graph4lg.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: chkstk_darwin 
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) 
Expected in: /usr/lib/libSystem.B.dylib 

dyld: Symbol not found: chkstk_darwin Referenced from: 
/usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: 
/usr/lib/libSystem.B.dylib 

Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics: 
pandoc document conversion failed with error 6
--- failed re-building ‘vignette_graph4lg.Rmd’ 

SUMMARY: processing the following file failed: 
‘vignette_graph4lg.Rmd’ 

Error: Vignette re-building failed. 
Execution halted 

- Besides, although I removed some unused packages from the imports in 
DESCRIPTION file, I still obtain this message : 

checking dependencies in R code ... NOTE Namespaces in Imports field not 
imported from: 
‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’ 
All declared Imports should be used. 

Except Rdpack which is needed to build the vignette, I removed these packages. 

Finally, although I submit version 0.4.0, I receive checking errors relative to 
version 0.3.0. 

I thank you in advance for your feedbacks. 
Regards
Paul Savary 







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