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

Brian G. Peterson brian at braverock.com
Thu Apr 20 10:57:06 CEST 2017


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.



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]]
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Brian G. Peterson
Ph: 773-459-4973
IM: bgpbraverock

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