Michael Hannon
2018-Feb-19 02:06 UTC
[R] 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
Ista Zahn
2018-Feb-19 02:15 UTC
[R] Include pre-existing PDF files as vignettes in an R package?
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.
Duncan Murdoch
2018-Feb-19 09:20 UTC
[R] Include pre-existing PDF files as vignettes in an R package?
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. >
Michael Hannon
2018-Feb-19 10:44 UTC
[R] Include pre-existing PDF files as vignettes in an R package?
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.
Michael Hannon
2018-Feb-19 10:47 UTC
[R] Include pre-existing PDF files as vignettes in an R package?
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. >> >
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