R help - Feb 2018 - Include pre-existing PDF files as vignettes in an R package?

Greetings.  The group that I work with has just started using the approach
outlined in Karl Broman's handy primer:

    http://kbroman.org/pkg_primer/pages/vignettes.html

to create vignettes for a couple of R packages.

This works fine as long as we have a current Rmd version of the vignette.  But
we have some old PDF documents that we'd like to include as vignettes as
well.
I'd like to know if there's a way to include such PDF files as
vignettes.

We *do* have the source files for the PDF files in question, but it would be
tedious to convert those source files to Rmd format.

My first thought was simply to add the PDF files to the .../vignettes
subdirectory and run the devtools::build_vignettes() function (mentioned in
the Broman tutorial), but that doesn't work.  I.e., the PDF files don't
appear
in the list of vignettes for the package.

And after running devtools::build_vignettes I see that there's a lot of
additional stuff in:

    ...lib/R/site-library/<package_name>/...

so I don't see any obvious way to "fool" R into using the PDF
files that
haven't gone through the whole knitr/rmarkdown process.  (Not to mention
that
such an approach would be fragile at best.)

Suggestions welcome.  Thanks.

-- Mike

Hi Mike,

Did you read the relevant section of the official "Writing R
Extensions" manual? If so, what about the instructions provided there
do you find lacking?

Best,
Ista

On Sun, Feb 18, 2018 at 9:06 PM, Michael Hannon
<jmhannon.ucdavis at gmail.com> wrote:
> Greetings.  The group that I work with has just started using the approach
> outlined in Karl Broman's handy primer:
>
>     http://kbroman.org/pkg_primer/pages/vignettes.html
>
> to create vignettes for a couple of R packages.
>
> This works fine as long as we have a current Rmd version of the vignette. 
But
> we have some old PDF documents that we'd like to include as vignettes
as well.
> I'd like to know if there's a way to include such PDF files as
vignettes.
>
> We *do* have the source files for the PDF files in question, but it would
be
> tedious to convert those source files to Rmd format.
>
> My first thought was simply to add the PDF files to the .../vignettes
> subdirectory and run the devtools::build_vignettes() function (mentioned in
> the Broman tutorial), but that doesn't work.  I.e., the PDF files
don't appear
> in the list of vignettes for the package.
>
> And after running devtools::build_vignettes I see that there's a lot of
> additional stuff in:
>
>     ...lib/R/site-library/<package_name>/...
>
> so I don't see any obvious way to "fool" R into using the PDF
files that
> haven't gone through the whole knitr/rmarkdown process.  (Not to
mention that
> such an approach would be fragile at best.)
>
> Suggestions welcome.  Thanks.
>
> -- Mike
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On 18/02/2018 9:06 PM, Michael Hannon wrote:
> Greetings.  The group that I work with has just started using the approach
> outlined in Karl Broman's handy primer:
> 
>      http://kbroman.org/pkg_primer/pages/vignettes.html
> 
> to create vignettes for a couple of R packages.
> 
> This works fine as long as we have a current Rmd version of the vignette. 
But
> we have some old PDF documents that we'd like to include as vignettes
as well.
> I'd like to know if there's a way to include such PDF files as
vignettes.
> 
> We *do* have the source files for the PDF files in question, but it would
be
> tedious to convert those source files to Rmd format.
> 
> My first thought was simply to add the PDF files to the .../vignettes
> subdirectory and run the devtools::build_vignettes() function (mentioned in
> the Broman tutorial), but that doesn't work.  I.e., the PDF files
don't appear
> in the list of vignettes for the package.
> 
> And after running devtools::build_vignettes I see that there's a lot of
> additional stuff in:
> 
>      ...lib/R/site-library/<package_name>/...
> 
> so I don't see any obvious way to "fool" R into using the PDF
files that
> haven't gone through the whole knitr/rmarkdown process.  (Not to
mention that
> such an approach would be fragile at best.)
You don't say what format the source is, but if it is LaTeX, you just 
need to add some comments at the beginning, rename ending in .Rnw, and R 
will recognize plain LaTeX files as Sweave vignettes.

See the Writing R Extensions manual, section 1.4.

Duncan Murdoch
> 
> Suggestions welcome.  Thanks.
> 
> -- Mike
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Heh.  Thanks, Ista, for your diplomatically-phrased suggestion :-)  In
fact, I *did* read the "vignettes" section of the Extensions manual,
but evidently not closely enough.

Upon further review, I see that one can use
".../vignettes/.install_extras" to list additional files that should
be copied to ".../inst/doc/".  I tried that, and it seems to work, but
the files from .install_extras are not listed as vignettes.

Hence, this seems like a convenient way to distribute the additional
files.  I.e., we would be asking people to use
"devtools::install_github" to get the packages, but I still don't
see
how to make the additional files readily available to the end user.

-- Mike

On Sun, Feb 18, 2018 at 6:15 PM, Ista Zahn <istazahn at gmail.com>
wrote:
> Hi Mike,
>
> Did you read the relevant section of the official "Writing R
> Extensions" manual? If so, what about the instructions provided there
> do you find lacking?
>
> Best,
> Ista
>
> On Sun, Feb 18, 2018 at 9:06 PM, Michael Hannon
> <jmhannon.ucdavis at gmail.com> wrote:
>> Greetings.  The group that I work with has just started using the
approach
>> outlined in Karl Broman's handy primer:
>>
>>     http://kbroman.org/pkg_primer/pages/vignettes.html
>>
>> to create vignettes for a couple of R packages.
>>
>> This works fine as long as we have a current Rmd version of the
vignette.  But
>> we have some old PDF documents that we'd like to include as
vignettes as well.
>> I'd like to know if there's a way to include such PDF files as
vignettes.
>>
>> We *do* have the source files for the PDF files in question, but it
would be
>> tedious to convert those source files to Rmd format.
>>
>> My first thought was simply to add the PDF files to the .../vignettes
>> subdirectory and run the devtools::build_vignettes() function
(mentioned in
>> the Broman tutorial), but that doesn't work.  I.e., the PDF files
don't appear
>> in the list of vignettes for the package.
>>
>> And after running devtools::build_vignettes I see that there's a
lot of
>> additional stuff in:
>>
>>     ...lib/R/site-library/<package_name>/...
>>
>> so I don't see any obvious way to "fool" R into using the
PDF files that
>> haven't gone through the whole knitr/rmarkdown process.  (Not to
mention that
>> such an approach would be fragile at best.)
>>
>> Suggestions welcome.  Thanks.
>>
>> -- Mike
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.

Thanks, Duncan.  The files in question are Emacs Org-mode files, and I
think these are more or less isomorphic to Rmd files, but I haven't
used Org-mode in a long time, so I think the mapping (Org-mode ==>
Rmd) would be painful.

-- Mike


On Mon, Feb 19, 2018 at 1:20 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> On 18/02/2018 9:06 PM, Michael Hannon wrote:
>>
>> Greetings.  The group that I work with has just started using the
approach
>> outlined in Karl Broman's handy primer:
>>
>>      http://kbroman.org/pkg_primer/pages/vignettes.html
>>
>> to create vignettes for a couple of R packages.
>>
>> This works fine as long as we have a current Rmd version of the
vignette.
>> But
>> we have some old PDF documents that we'd like to include as
vignettes as
>> well.
>> I'd like to know if there's a way to include such PDF files as
vignettes.
>>
>> We *do* have the source files for the PDF files in question, but it
would
>> be
>> tedious to convert those source files to Rmd format.
>>
>> My first thought was simply to add the PDF files to the .../vignettes
>> subdirectory and run the devtools::build_vignettes() function
(mentioned
>> in
>> the Broman tutorial), but that doesn't work.  I.e., the PDF files
don't
>> appear
>> in the list of vignettes for the package.
>>
>> And after running devtools::build_vignettes I see that there's a
lot of
>> additional stuff in:
>>
>>      ...lib/R/site-library/<package_name>/...
>>
>> so I don't see any obvious way to "fool" R into using the
PDF files that
>> haven't gone through the whole knitr/rmarkdown process.  (Not to
mention
>> that
>> such an approach would be fragile at best.)
>
>
> You don't say what format the source is, but if it is LaTeX, you just
need
> to add some comments at the beginning, rename ending in .Rnw, and R will
> recognize plain LaTeX files as Sweave vignettes.
>
> See the Writing R Extensions manual, section 1.4.
>
> Duncan Murdoch
>
>>
>> Suggestions welcome.  Thanks.
>>
>> -- Mike
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>