[R-pkg-devel] Fixed for messages

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Mon Jan 8 20:17:30 CET 2018


Just to complete the record,  the suggested fixes did indeed fix things, and as I said Henrik provided a clear explanation of why the results are different in R-devel.

Thanks again,

-Roy



> On Jan 8, 2018, at 9:28 AM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
> 
> Thanks.  What I have at the top of my Vignette is:
> 
>> output: 
>> rmarkdown::html_vignette: default
>> 
>> vignette: >
>>  %\VignetteIndexEntry{Usingxtractomatic}
>>  %\VignetteEngine{knitr::rmarkdown}
>>  \usepackage[utf8]{inputenc}
>> ---
>> 
> 
> It is based on the template in RStudio when you choose a vignette as the file.  I have added rmarkdown as well as webshot to my suggests,  and sent to win-builder-devel,  will see what happens.
> 
> Thanks,
> 
> -Roy
> 
> 
> 
>> On Jan 8, 2018, at 9:17 AM, Thierry Onkelinx <thierry.onkelinx at inbo.be> wrote:
>> 
>> Dear Roy,
>> 
>> Make sure that in DESCRIPTION you have at least
>> 
>> Suggests: knitr, rmarkdown
>> VignetteBuilder: knitr
>> 
>> The vignette requires
>> 
>> %\VignetteEngine{knitr::rmarkdown}
>> 
>> webshot is used by rmarkdown or knitr to convert dynamic HTML output
>> to a static image when the output is not HTML. Are you using pdf as
>> output format for the vignette? Consider using
>> rmarkdown::html_vignette.
>> 
>> Best regards,
>> 
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>> 
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkelinx at inbo.be
>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be
>> 
>> ///////////////////////////////////////////////////////////////////////////////////////////
>> To call in the statistician after the experiment is done may be no
>> more than asking him to perform a post-mortem examination: he may be
>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does
>> not ensure that a reasonable answer can be extracted from a given body
>> of data. ~ John Tukey
>> ///////////////////////////////////////////////////////////////////////////////////////////
>> 
>> 
>> 
>> 
>> 2018-01-08 17:40 GMT+01:00 Roy Mendelssohn - NOAA Federal
>> <roy.mendelssohn at noaa.gov>:
>>> Thanks Henrik:
>>> 
>>> I am a little slow,  I want to make certain I do this correctly.  I already have knitr in my Suggests,  and the message is:
>>> 
>>>>>> knitr::rmarkdown
>>> 
>>> So do I put in my Suggests list  rmarkdown or knitr::rmarkdown
>>> 
>>> And most importantly,  thanks for the explanation about what is happening with R-devel.  Of the responses I have seen,  it is the first one (at least to me) that is clear what is going on to cause the errors,  and how to approach correcting them.
>>> 
>>> -Roy
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote:
>>>> 
>>>> On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
>>>> <roy.mendelssohn at noaa.gov> wrote:
>>>>> Hi All:
>>>>> 
>>>>> In tesitng a package on winbuild-devel (but not on release)  I get the following errors or warnings:
>>>>> 
>>>>>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>>>>>> The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
>>>>>> 
>>>>> 
>>>>> There was an email about this a few days ago,  but then,  as now,  it is not clear to me specifically what I need to do where so that I don't get this warning.  Do I need to include rmarkdown in the Suggests,
>>>> 
>>>> Yes, add it to Suggests.
>>>> 
>>>> or do I need to do something specific in the Vignette.  Or is this
>>>> just a question that winbuild hasn't installed it yet in the
>>>> development version and I can ignore it for now?
>>>>> 
>>>>> Also I am getting this error (again only in the development version):
>>>>> 
>>>>>> Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
>>>>>> there is no package called 'webshot'
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> Now I don't explicitly use a package called 'webshot',  but the lines referenced in the error message are:
>>>>> 
>>>>>> require("DT")
>>>>>> DT::datatable(searchResult)
>>>>>> 
>>>>> 
>>>>> where "searchResult" is just a list.   DT itself does not explicitly import "webshot" either.
>>>> 
>>>> It most likely depend on 'webshot' indirectly through some of your
>>>> package dependencies.  So, add this one too to Suggests.
>>>> 
>>>> As far as I understand it, the new R-devel tests basically tests your
>>>> package with the minimal setup of packages (a "sandboxed" .libPaths())
>>>> inferred from you DESCRIPTION (by excluding Suggests of the packages
>>>> you depend on, which is where I think 'webshot' lives).
>>>> 
>>>> /Henrik
>>>> 
>>>>> 
>>>>> I would like to submit this package,  but I don't want to submit with any errors or warnings. Again,  I only get these on winbuild-devel.
>>>>> 
>>>>> Thanks for any help.
>>>>> 
>>>>> -Roy
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> **********************
>>>>> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
>>>>> **********************
>>>>> Roy Mendelssohn
>>>>> Supervisory Operations Research Analyst
>>>>> NOAA/NMFS
>>>>> Environmental Research Division
>>>>> Southwest Fisheries Science Center
>>>>> ***Note new street address***
>>>>> 110 McAllister Way
>>>>> Santa Cruz, CA 95060
>>>>> Phone: (831)-420-3666
>>>>> Fax: (831) 420-3980
>>>>> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
>>>>> 
>>>>> "Old age and treachery will overcome youth and skill."
>>>>> "From those who have been given much, much will be expected"
>>>>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>>>>> 
>>>>> ______________________________________________
>>>>> R-package-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>> 
>>> **********************
>>> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
>>> **********************
>>> Roy Mendelssohn
>>> Supervisory Operations Research Analyst
>>> NOAA/NMFS
>>> Environmental Research Division
>>> Southwest Fisheries Science Center
>>> ***Note new street address***
>>> 110 McAllister Way
>>> Santa Cruz, CA 95060
>>> Phone: (831)-420-3666
>>> Fax: (831) 420-3980
>>> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
>>> 
>>> "Old age and treachery will overcome youth and skill."
>>> "From those who have been given much, much will be expected"
>>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>>> 
>>> ______________________________________________
>>> R-package-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
> 
> **********************
> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
> 
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected" 
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> 

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.



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