similar to: Seeking Packaging advice

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:

Interesting, yesterday I had exactly this problem, but today I solved it (see the R-pkg-devel list) by _installing_ R-devel and > update.packages(checkBuilt = TRUE) I also tried it on Martin's Fedora 26 example below. Worked fine (had to install some packages...) On ubuntu 16.04. G?ran Brostr?m On 2017-12-06 11:29, Martin Maechler wrote: >>>>>> Pearce, Robert

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

Hi, Could R-Core consider adding 'RtangleRuncode' and 'RtangleFinish' to the exports of utils. Their weave equivalent 'makeRweaveLatexCodeRunner' and ?'RweaveLatexFinish' are exported, as well as the other tangle utility functions 'RtangleSetup' and 'RtangleWritedoc'. The rationale is not just symmetry. ;-) I'm finishing a small package that

I have 3 questions about creating a package for R, and would appreciate any guidance. 1. Demonstrating the packaged code requires some support code files. It would seem natural to put these in the demo directory, but "Writing R extensions" says files in demo should be suitable for runing from demo(). The support files are not intended to be run from the top level. How should I handle

I am resubmitting this bug report but with additional information. I am running this with windows 10: w64-mingw32 with R Under development (unstable) (2017-12-04 r73829). I build 'httk' from the command prompt using 'R CMD build httk' after installing the required packages. Then when the vignettes are being created, it crashes. Today I installed the latest versions of Rtools,

>>>>> Pearce, Robert <Pearce.Robert at epa.gov> >>>>> on Tue, 5 Dec 2017 21:31:09 +0000 writes: > I am resubmitting this bug report but with additional information. I am running this with windows 10: w64-mingw32 with R Under development (unstable) (2017-12-04 r73829). There is no such message (as you cite below) in the R-devel archives:

Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved. It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release. See the complete thread

Robert, To expand a bit on Goran's point, is it possible that you have an old library with packages installed that your R-devel is hitting. The R headers changes relatively recently, so any packages with compiled code that were built long enough ago (I don't have the exact date off the top of my head) need to be rebuilt before they can be safely used. If this is happening in a state

Hi, Here is a summary of the replies to my question yesterday about documenting a long function with Sweave. My thanks to those who replied. Friedrich Leisch suggested a work around which was copied to the mailing list so I wont repeat it here. This worked well. (I made a minor addition by adding braces around each chunk of code to make the output in the pdf file look a bit prettier. This seems

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,

If I understand correctly, all vignettes in a package are built in the same R process. Global options, loaded packages, etc., in an earlier vignette persist in later vignettes. This can introduce user confusion (e.g., when a later vignette builds successfully because a package is require()'ed in an earlier vignette, but not the current one), difficult-to-identify bugs (e.g., when a setting

In Section 1.4.2 of "Writing R Extensions" %\VignetteEngine{knitr::knitr} should be %\VignetteEngine{knitr::knit} > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) Is this sort of thing best reported here, or is a huge report in order? John Maindonald email: john.maindonald at anu.edu.au phone : +61 2 (6125)3473 fax

Hello, I'm trying to rebuild a package (using R version 3.3.2 (2016-10-31)) that has not seen any changes since it was last built without problems in previous R versions. It fails during vignette building with: ---<--------------------cut here---------------start------------------->--- $ R CMD build diveMove * checking for file ?diveMove/DESCRIPTION? ... OK * preparing ?diveMove?: *

Dear list Getting very frustrated with this simple-looking problem > m1 <- lm(x~y, data=mydata) > outliers <- abs(stdres(m1))>2 > plot(x~y, data=mydata) I would like to plot a simple x,y scatter plot with labels giving custom information displayed for the outliers only, i.e. I would like to define a column mydata$labels for the mydata dataframe so that the command >

thanks for the reply, Phil It would, were udev not inserting USB and/or eSATA drives at /dev/sdb1 and/or /dev/sdc1 and exposing the array to the udev rule intended to handle only removable devices (at sdc or sdd). The array then mounts unpredictably in /media/xxx-sdc1 or sdd1 - not what is wanted - depend on how many removable devices are plugged at the time of rebooting. Of course, a single

So far you haven't provided a reproducible example yet. I wonder what exactly the object `sample_analysis` is. Sounds like it is an environment. If that is the case, devtools::build_vignettes() will tangle (for the meaning of "tangle", see ?tools::buildVignette) your vignette into an invalid R script. Environments cannot be represented via dput(), so knitr's purl() (eventually

Sometimes you want to compute the physical size of a plot based on data. In R itself this is no problem. But is there a way to compute the values of height and width in S-weave, say: <<graph,fig=TRUE,height=xx,width=yy>>= where xx and yy are computed and not physically written in the document? Bendix ______________________________________________ Bendix Carstensen Senior

Thanks Brian. Indeed, the vignette is in markdown form. When I updated my system to R 3.1.3 I ran update.packages() and this seems to have upset things (including R-studio processing of markdown files). I tried removing rmarkdown and reverting to an older version so that my sessionInfo() is Loading required package: rmarkdown > sessionInfo() R version 3.1.3 (2015-03-09) Platform:

In trying to change the driver used by Sweave on the command line using R CMD Sweave --driver=foo I consistently get the "directory 'foo' does not exist' error. (For any value of 'foo', even the default 'RweaveLatex'.) Looking up the source code for function .Sweave that is called by 'R CMD Sweave', I notice that the argument 'driver', if