similar to: do not eval vignettes during R CMD build

Hi, Recently I saw a couple of cases in which the package vignettes were somewhat complicated so that Stangle() (or knitr::purl() or other tangling functions) can fail to produce the exact R code that is executed by the weaving function Sweave() (or knitr::knit(), ...). For example, this is a valid document that can pass the weaving process but cannot generate a valid R script to be source()d:

Dear R-helpers, www.statistik.lmu.de/~*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf says that R CMD build creates the pdf from a .Rnw file. But when I do R CMD build followed by R CMD check it gives me a warning that there is a vignette without a PDF. My query is : when R CMD build works it creates a pdf in the doc subdirectory of the directory returned by system.file(package = mypackage) and not

Hi, I have a package that contains two vignettes that both use saved objects in the examples directory of the package. With previous versions of R I could have a code chunk in the vignette like this: <<echo=false>>= load("../examples/somedata.Rdata") @ followed by a code chunk like <<eval=false>>= foo <- bar("data") @ that simulated the actual

Now that R 3.0.0+ supports non-Sweave vignettes, R-exts \S 1.4.2 seems to imply that it is possible to include both Sweave and knitr vignettes in a single package. I'm wondering if anyone has tried this and/or if there are some hidden gotchas putting this into practice, and concerned about creating problems with CRAN checks if I try this. Consider two vignettes: pkg/vignettes/vign1.Rnw,

As a user, I am always annoyed beyond measure that Sweave vignettes precede the code by a command line prompt. It makes running examples by simple copying of the commands from the vignette to the console a pain. I know the idea is that it is clear what is the command, and what is the output, but I'd rather precede the output with some kind of marking. Is there any other solution possible /

Hi, is it possible to have non-Sweave vignettes(*) in inst/doc/ be listed under 'Downloads' on CRAN package pages? For instance, in my R.rsp package I have a inst/doc/report.pdf (part of the source *.tar.gz) that is not detected/listed. The PDF is not based on a Sweave vignette but an *.tex.rsp vignette that is dynamically created via inst/doc/Makefile. It is listed (*) BTW, can the

Hi, I found the following problem with recent R-devel (2010-08-26 r52817) on Windows (32-bit and 64-bit): 'R CMD build <pkg>' gets stalled during vignette creation for packages that have a Makefile in <pkg>/inst/doc. It seems that the problem is that the commands used in the Makefile for converting .tex to .pdf are not able to locate the Sweave.sty file anymore (if I drop

In R 3.1.0 (~April 2014), support for vignettes in inst/doc/ will go away (and probably much sooner for CRAN submission), e.g. checking for old-style vignette sources ... NOTE Vignette sources only in ?inst/doc?: ?R.devices-overview.tex.rsp? A ?vignettes? directory is required as from R 3.1.0 and these will not be indexed nor checked I've been sticking with inst/doc/ for backward compatible

It is stated in R-exts that Sweave files (.Rnw) are either processed in /vignettes or /inst/doc, not both. Furthermore, it is stated that external manuals and other files in /inst/doc will be installed. This behaviour has been used to deal with the situation where a package has two "vignettes", one that is easily processed and one that has a long running time. This could be done by

I haven't figured it out entirely, but it looks like there are a couple of small glitches with knitr-based vignettes and SweaveParseOptions. I posted the tarball of a package with a knitr vignette with (as far as I can tell) everything properly coded in the DESCRIPTION file (VignetteBuilder: knitr, Suggests: knitr) and the vignette itself (%\VignetteEngine{knitr::knitr}). When Windows

I would like R CMD build to run some R code which does some stuff and save the result as a file in /inst/docs folder. Is there any way of doing this. Thank you. Johan ____________________________________________________________________________________ We won't tell. Get more on shows you hate to love [[alternative HTML version deleted]]

Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: "Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]". In my package,

Hi, I want to have a "vignette" in one of my R packages. Hence, I added an Sweave file into the /inst/doc subdirectory of this package. Unfortunately, 'R CMD check' gives a warning: ========================================== [...] * checking tests ... OK * checking package vignettes in 'inst/doc' ... WARNING --- f?hre texi2dvi auf Vignetten aus * creating

Hi, as far as I understand it, the new R devel feature of processing non-Sweave vignettes will (a) locate any "[.][RrSs](nw|tex)$" or ".Rmd" files, (b) check for a registered vignette engine, (c) process the file using the registered "weave" function, (d) and possibly post process the generated weave artifact (e.g. a *.tex file). I'd like to propose to extend

Hello I am trying to evaluate an Incomplete gamma function in R. Library Zipfr gives the Igamma function. From Mathematica, I have: "Gamma[a, z] is the incomplete gamma function." In[16]: Gamma[9,11.1] Out[16]: 9000.5 Trying the same in R, I get > Igamma(9,11.1) [1] 31319.5 OR > Igamma(11.1,9) [1] 1300998 I know I have to understand the theory and the math behind it rather

Dear list, On Fedora 8 I downloaded the beta version of R via svn. make and make check-all worked fine, but make vignettes is failing with: make[1]: Entering directory `/home/gavin/R/2-7-patched/build/src/library' building/updating vignettes for package 'grid' ... processing 'displaylist.Snw' /usr/bin/texi2dvi: pdflatex exited with bad status, quitting. Error in

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: >>

Dear R developers, I had some problem when building package: for exemple when building the package e1071 available from CRAN, I get the following message error: * checking for file 'e1071/DESCRIPTION' ... OK * preparing 'e1071': * cleaning src * running cleanup * creating vignettes ... ERROR /usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.

During vignette generation on Windows, Sweave seems to clean up before all graphics files are completely processed. For instance, if tmp.Rnw is: \documentclass[12pt]{article} \begin{document} <<>>= bitmap("afile.png") plot(1:100) dev.off() @ \end{document} Then: C:\R\tmp>R CMD Sweave tmp.Rnw Writing to file tmp.tex Processing code chunks ... 1 : echo term verbatim

On 19/02/2018 5:47 AM, Michael Hannon wrote: > 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. If they aren't LaTeX then they won't be able to masquerade as Sweave files, so things are