[R-pkg-devel] R CMD check not finding my vignettes

Thu Apr 20 15:58:03 CEST 2017

Hi guys,

Thanks very much for all of your comments. I now have a good sense of what
the possibilities are, and I will think about what works best for my
package.

Cheers,
David

On 20 April 2017 at 14:42, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

> On 20/04/2017 4:57 AM, Brian G. Peterson wrote:
>
>> David,
>>
>> I'd suggest creating a vignette for each of HTML and PDF, and including
>> a source file that contains the common code.  e.g. have a pdf header and
>> an html header file, and then include the 'main' Rmd as a child doc from
>> each header Rmd.  This way R CMD build could build both pdf and html
>> versions of the output.
>>
>
> That's another solution.  My suggestion would be simpler:  just pick one
> of PDF or HTML, and give the user instructions to produce the other if
> necessary, but don't produce it for them.
>
> Duncan Murdoch
>
>
>
>> Regards,
>>
>> Brian
>>
>> On 04/20/2017 03:38 AM, David Hugh-Jones wrote:
>>
>>> Hi Duncan,
>>>
>>> Thank you very much for taking the time to look at this.
>>>
>>> I tried rebuilding the tar file so as to include only the .Rmd files, not
>>> the HTML files, in 'vignettes':
>>>
>>> drwxr-xr-x  0 david  staff       0 20 Apr 09:21 huxtable/vignettes/
>>>
>>> -rw-r--r--  0 david  staff    1633  6 Apr 16:26
>>> huxtable/vignettes/comparison.csv
>>>
>>> -rw-r--r--  0 david  staff    6697  6 Apr 14:44
>>> huxtable/vignettes/design-principles.Rmd
>>>
>>> -rw-r--r--  0 david  staff    5521  6 Apr 14:30
>>> huxtable/vignettes/huxreg.Rmd
>>>
>>> -rw-r--r--  0 david  staff   20552  6 Apr 16:19
>>> huxtable/vignettes/huxtable.Rmd
>>>
>>> -rw-r--r--  0 david  staff      22 17 Mar 00:19
>>> huxtable/vignettes/placeins-header.tex
>>>
>>>
>>> But when I run R CMD check, I still get the same warning:
>>>
>>> * checking package vignettes in ‘inst/doc’ ... WARNING
>>>
>>> Package vignettes without corresponding PDF/HTML:
>>>
>>>    ‘design-principles.Rmd’
>>>
>>>    ‘huxreg.Rmd’
>>>
>>>    ‘huxtable.Rmd’
>>>
>>> So, the warning does not seem to be related to the presence of HTML files
>>> in vignettes.
>>>
>>> I also tried manually removing .Rmd files from inst/doc (leaving them
>>> only
>>> in vignettes) but this still gave the same error.
>>>
>>> My goal here is that for package-specific reasons, I would like both pdf
>>> and HTML versions of my vignettes to be available (I am writing code that
>>> prints HTML and LaTeX tables and want my users to have examples of how
>>> both
>>> output formats work). This is why I build those files manually, and place
>>> them in inst/doc.
>>>
>>> Side comment: at the moment, I feel as if I am running through the
>>> combinatorics of including and excluding files from vignettes and
>>> inst/doc,
>>> without much insight into what I am doing. Would it be fair to say that
>>> the
>>> current system is not very easy to comprehend?
>>>
>>> Cheers,
>>>
>>> David
>>>
>>> On 19 April 2017 at 21:24, Duncan Murdoch <murdoch.duncan at gmail.com>
>>> wrote:
>>>
>>> On 19/04/2017 1:00 PM, David Hugh-Jones wrote:
>>>>
>>>> Hi Uwe,
>>>>>
>>>>> I'm not sure if you ever got my off-list message with my tarball or
>>>>> subsequent messages. I can't send a tarball on-list - it gets rejected
>>>>> as
>>>>> too large - but here is a dropbox link. If you could confirm receipt,
>>>>> that
>>>>> would be extremely helpful!
>>>>>
>>>>> https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0
>>>>>
>>>>>
>>>>> Not sure if Uwe has had a chance to look, but I just ran R CMD check on
>>>> your tarball using the latest version of R-devel.  It reported the
>>>> following problems:
>>>>
>>>> * checking CRAN incoming feasibility ... NOTE
>>>> Maintainer: ‘David Hugh-Jones <davidhughjones at gmail.com>’
>>>>
>>>> Found the following (possibly) invalid URLs:
>>>>   URL: http://cran.rstudio.com/web/packages/huxtable/index.html
>>>>     From: README.md
>>>>     CRAN URL not in canonical form
>>>>   Canonical CRAN.R-project.org URLs use https.
>>>>
>>>> The URL for your package should be in the form
>>>>
>>>> https://CRAN.R-project.org/package=huxtable
>>>>
>>>> * checking top-level files ... NOTE
>>>> Non-standard file/directory found at top level:
>>>>   ‘multirow.rds’
>>>>
>>>> I'm not sure where that file belongs, but not there.
>>>>
>>>> * checking files in ‘vignettes’ ... WARNING
>>>> Files in the 'vignettes' directory newer than all files in 'inst/doc':
>>>>   ‘huxreg.html’, ‘huxtable.html’
>>>>
>>>> Those files shouldn't be in the vignettes directory, they are products
>>>> of
>>>> building the vignettes.  Only the source should normally be in the
>>>> vignettes directory.
>>>>
>>>> * checking package vignettes in ‘inst/doc’ ... WARNING
>>>> Package vignettes without corresponding PDF/HTML:
>>>>    ‘design-principles.Rmd’
>>>>    ‘huxreg.Rmd’
>>>>    ‘huxtable.Rmd’
>>>>
>>>> I think this is the warning you were asking about.  If I look at just
>>>> the
>>>> first of those files, I see that design-principles.Rmd exists in
>>>> vignettes
>>>> and is set to produce PDF output (only the first output entry in the
>>>> YAML
>>>> counts).  You also have a .html file in vignettes; it shouldn't be
>>>> there.
>>>> In inst/doc, you have source, .html and .pdf versions of that file.
>>>>
>>>> The warning isn't very helpful, but I think it is triggered by the fact
>>>> that you've got the .html file in your vignettes directory.  If I remove
>>>> everything but the source from that directory, and everything from the
>>>> inst/doc directory, then all the vignette warnings go away.
>>>>
>>>> (I haven't traced through the code, but I think the warning may be
>>>> literally correct.  Since you had .html files that looked like vignette
>>>> outputs but weren't, you have vignettes without *corresponding* HTML. It
>>>> would have been nicer if it suggested how to fix this, but that vignette
>>>> code is quite tricky, because any file could be source, and any html,
>>>> tex
>>>> or pdf file could be output.  At some point I may try to clean it up a
>>>> bit
>>>> and then maybe the error messages will be less obscure.)
>>>>
>>>> Duncan Murdoch
>>>>
>>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-package-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>>
>>
>>
> ______________________________________________
> R-package-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

	[[alternative HTML version deleted]]