Re: [Rd] Vignettes with long compute time

On 11/03/2024 11:43 a.m., Therneau, Terry M., Ph.D. via R-devel wrote: Is there a way to include the compiled version of a vignette in the doc directory but mark it to NOT be rerun by CRAN?   I think I remember that this is possible, but have forgotton how.   (It might even be a false memory.)

Re: [Rd] Vignettes with long compute time

> Is there a way to include the compiled version of a vignette in the doc directory but mark it to NOT be rerun by CRAN? Some developers "precompute" their vignettes so CRAN has nothing left to run: https://ropensci.org/blog/2019/12/08/precompute-vignettes/ > Beth Atkinson and I are splitting out

[Rd] Vignettes with long compute time

Is there a way to include the compiled version of a vignette in the doc directory but mark it to NOT be rerun by CRAN?   I think I remember that this is possible, but have forgotton how.   (It might even be a false memory.) Terry T. Background:  Beth Atkinson and I are splitting out many of t

Re: [Rd] vignettes present in 2 folders or won't work

is that it wipes out inst/doc (but it does ask for confirmation). Georgi Boshnakov -- Message: 12 Date: Mon, 2 Nov 2020 05:22:02 -0500 From: Duncan Murdoch To: Mark van der Loo Cc: Dirk Eddelbuettel , r-devel Subject: Re: [Rd] vignettes present in 2 f

Re: [Rd] vignettes present in 2 folders or won't work

On 02/11/2020 4:07 a.m., Mark van der Loo wrote: On Sun, Nov 1, 2020 at 10:39 PM Duncan Murdoch > wrote: On 01/11/2020 2:57 p.m., Dirk Eddelbuettel wrote: > > The closest to a canonical reference for a static vignette is the basic blog >

Re: [Rd] vignettes present in 2 folders or won't work

On Sun, Nov 1, 2020 at 10:39 PM Duncan Murdoch wrote: > On 01/11/2020 2:57 p.m., Dirk Eddelbuettel wrote: > > > > The closest to a canonical reference for a static vignette is the basic > blog > > post by Mark at > > > > > https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-

Re: [Rd] vignettes present in 2 folders or won't work

On 01/11/2020 2:57 p.m., Dirk Eddelbuettel wrote: The closest to a canonical reference for a static vignette is the basic blog post by Mark at https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ which I follow in a number of packages. Back to the origina

Re: [Rd] vignettes present in 2 folders or won't work

CRAN policies say, "neither data nor documentation should exceed 5MB (which covers several books). A CRAN package is not an appropriate way to distribute course notes, and authors will be asked to trim their documentation to a maximum of 5MB."[1] I post R Markdown vignettes as companion

Re: [Rd] vignettes present in 2 folders or won't work

The closest to a canonical reference for a static vignette is the basic blog post by Mark at https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ which I follow in a number of packages. Back to the original point by Alexandre: No, I do _not_ think we can do

Re: [Rd] vignettes present in 2 folders or won't work

I take Duncan's point but would second the motion to have WRE clarify how static vignettes are supposed to work; it's a topic I am repeatedly confused about despite being an experienced package maintainer. If knowledgeable outsiders compiled a documentation patch would it be likely to be cons

Re: [Rd] vignettes present in 2 folders or won't work

On 01/11/2020 1:02 p.m., Alexandre Courtiol wrote: Noted Duncan and TRUE... I cannot do more immediately unfortunately, that is always the issue of asking a last minute panic attack question before teaching a course involving the package... I do have /doc in my .Rbuildignore for reasons I can

Re: [Rd] vignettes present in 2 folders or won't work

Noted Duncan and TRUE... I cannot do more immediately unfortunately, that is always the issue of asking a last minute panic attack question before teaching a course involving the package... I do have /doc in my .Rbuildignore for reasons I can no longer remember... I will dig and create a MRE/repre

Re: [Rd] vignettes present in 2 folders or won't work

You are doing a lot of things that are non-standard, so I doubt if anyone is going to be able to help you without access to a simple reproducible example of a package that does what you do. Try to cut out as much as you can to make it minimal. For example, devtools::document() (indeed, most o

[Rd] vignettes present in 2 folders or won't work

Dear all, I am struggling with an issue related to static vignettes: they work, but only when present in double in the tarball -- in the folder inst/doc and vignettes; see below for details. Details: I am pre-compiling heavy vignettes thanks to the vignette builder R.rsp. So basically, I have PD

Re: [Rd] vignettes with similar names

On 28/02/2014 04:25, Michael Sumner wrote: In R 3.0.2 Patched (2014-01-31 r64905) and 3.0.3 beta (2014-02-25 r65077) I see a problem loading vignettes when I create a package with two vignettes with similar names, e.g. "vignette3" "vignette3-install" These seem not to be distinguished, and I ge

[Rd] vignettes with similar names

In R 3.0.2 Patched (2014-01-31 r64905) and 3.0.3 beta (2014-02-25 r65077) I see a problem loading vignettes when I create a package with two vignettes with similar names, e.g. "vignette3" "vignette3-install" These seem not to be distinguished, and I get this vignette("vignette3") vignette ‘vigne

Re: [Rd] vignettes: problems with PDF compaction

On 4/22/2013 5:51 PM, Uwe Ligges wrote: But this doesn't do anything, not even changing the timestamp on the file, because the file size doesn't change enough. Either you changed it or not, there is no "not enough". I meant that the code in tools::compact compares the sizes of the old and new

Re: [Rd] vignettes: problems with PDF compaction

It's certainly not obvious, but you should use 'gswin32c.exe' instead of 'gswin32.exe'. From http://ghostscript.com/doc/current/Install.htm#Install_Windows "GSWIN32C.EXE Ghostscript as a 32-bit Windows command line program. This is usually the preferred executable. GSWIN32.EXE 32-bit Ghostscript

Re: [Rd] vignettes: problems with PDF compaction

On 22.04.2013 17:59, Michael Friendly wrote: On 4/21/2013 1:28 PM, Michael Friendly wrote: [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpd

Re: [Rd] vignettes: problems with PDF compaction

On 4/21/2013 1:28 PM, Michael Friendly wrote: [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpdf’ made some significant size reductions:

Re: [Rd] vignettes: problems with PDF compaction

On 4/21/2013 1:47 PM, Uwe Ligges wrote: >> Since vignettes are re-built from sources and then installed into >> inst/doc, I don't see why >> PDF compaction cannot be run as part of the build process. That is, if >> R CMD check --as-cran detects a problem, shouldn't there be some >> option for >> R

Re: [Rd] vignettes: problems with PDF compaction

On 21.04.2013 19:28, Michael Friendly wrote: [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpdf’ made some significant size reductions:

[Rd] vignettes: problems with PDF compaction

[Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpdf’ made some significant size reductions: compacted ‘HE-examples.pdf’ from 739Kb to 366Kb

Re: [Rd] Vignettes are not being (re)built.

On 22/06/2012 23:01, Jeff Hamann wrote: I'm adding a couple of vignettes to an existing package. Incorrectly, it seems, but you told us no details. You can use R CMD build to get the PDFs (re-)built. R CMD check checks (preferably the tarball), but re-makes nothing. When I make a change

[Rd] Vignettes are not being (re)built.

I'm adding a couple of vignettes to an existing package. When I make a change to the sweave file, and run the check command, c:\conifers\trunk>R CMD check rconifers I get the following message(s) in the 00check.log file: * checking for unstated dependencies in vignettes ... OK * checking pack

[Rd] Vignettes and CRAN checks

I'l like to chime in on the subject of vignette checks. I have one vignette in the coxme library that would be better described as a white paper. It discusses the adequacy of the Laplace transform under various scenarios. It contains some substantial computations, so I'd like to mark it as "ne

[Rd] vignettes/

I am experimenting with putting vignettes in a vignettes/ directory as suggested in the new R release news. If I understand correctly, it is now suggested that the vignette source (.Stex in my case) should be in the vignettes/ directory and the pdf should be put in the inst/doc/ directory, for

[Rd] vignettes processed twice under Windows?

When I try to build vignettes for a package under Windows the package shared library is built twice, first presumably to generate the vignette, and then to generate the package binary. But the library building steps are of course the same. Is this a known issue or is there a way to get it to build

Re: [Rd] Vignettes with missing or empty \VignetteIndexEntry:

> Christophe Dutang writes: > Hi, > I have a problem when checking the package 'probdistr' (on probability > distributions). > I got this warning > * checking index information ... WARNING > Vignettes with missing or empty \VignetteIndexEntry: > [1] "probdistr-chi""probdistr-conte

[Rd] Vignettes with missing or empty \VignetteIndexEntry:

Hi, I have a problem when checking the package 'probdistr' (on probability distributions). I got this warning * checking index information ... WARNING Vignettes with missing or empty \VignetteIndexEntry: [1] "probdistr-chi""probdistr-contextra" "probdistr-discrete" [4] "probdistr-d

Re: [Rd] vignettes in a bundle

Romain Francois wrote: Would this work better: <>= bib <- system.file( "doc", "bayesian.bib", package = "emulator" ) cat( "\\bibliography{",bib,"}\n",sep='') @ Romain Yes, this gives cleaner TeX output (I keep on forgetting about Sweave's 'result' code chunk option). But I still don't unders

Re: [Rd] vignettes in a bundle

Would this work better: <>= bib <- system.file( "doc", "bayesian.bib", package = "emulator" ) cat( "\\bibliography{",bib,"}\n",sep='') @ Romain Robin Hankin wrote: Hello Romain this is brilliant; it never occurred to me to use cat() in this way. It works but I don't know why. With: <>= bib

Re: [Rd] vignettes in a bundle

Hello Romain this is brilliant; it never occurred to me to use cat() in this way. It works but I don't know why. With: <>= bib <- system.file( "doc", "bayesian.bib", package = "emulator" ) cat( "\\bibliography{",bib,"}\n",sep='') @ in the Rnw file, the TeX file looks like this: \begin{Schunk

Re: [Rd] vignettes in a bundle

Hi Robin, Something like: <>= bib <- system.file( "bib", "mybib.bib", package = "yada" ) cat( "\\bibliography{",bib,"}\n") @ It would also be nice to be able to use bibliography in Rd files ... Romain Robin Hankin wrote: Hi I have a bundle comprising three packages. Each package has a vign

[Rd] vignettes in a bundle

Hi I have a bundle comprising three packages. Each package has a vignette. Currently each vignette has a separate .bib file. How do I arrange the bundle so that each vignette accesses a single, common, .bib file? thanks Robin -- Robin K. S. Hankin Uncertainty Analyst University of Cambridg

Re: [Rd] vignettes and papers

Robin: > Lots of my packages have been the subject of > journal articles either in JSS or Rnews or (in one > case) elsewhere. > > I would like to add these articles > to my packages as vignettes. > > Reproducing the papers exactly requires a number > of files [such as style files or PDFs] to be in

[Rd] vignettes and papers

Hello everyone Lots of my packages have been the subject of journal articles either in JSS or Rnews or (in one case) elsewhere. I would like to add these articles to my packages as vignettes. Reproducing the papers exactly requires a number of files [such as style files or PDFs] to be included i