similar to: 'library(ggplot2)' R CMD check WARNING in vignette R code

Hello, sorry for not being clear enough. My problem is represented with the following code, running on OSX: mkdir ~/test ln -s ~/test ~/testlink touch ~/test/foo Rscript -e 'Sys.readlink(c("~/test/foo", "~/testlink/foo")); normalizePath(c("~/test/foo","~/testlink/foo"))' I expected `Sys.readlink` to show the same output as `normalizePath`. Also,

Hello together, the function `Sys.readlink` uses the system's readlink command to resolve symlink paths. On OSX/BSD the command has a different meaning than on Linux [1]. There exists the tool 'realpath', which seems suitable for the task, at least applied at the command line level [2]. It is used in `normalizePath`. I suggest (at least the latter) to * use realpath instead readlink

Dear developers, the implementation of S4 generics for existing S3 ones in the base package is concerned to be a threat to quick startup times [1]. But since S4 is promoted, and S3/S4 interoperability a pain when package developing [2], are there efforts to improve the situation? E.g. an S3 free system, etc. A good thing [2] is the package 'stats4', including some setGeneric calls (e.g.

Hello, I wrote a function to show the help/index page of a package in a browser (and want to include this in an update for a CRAN package). I asked in R-help how to obtain the 00Index.html file, Duncan Murdoch suggested to inspect (see http://r.789695.n4.nabble.com/Obtain-00Index-html-tt4697661.html) tools:::httpd (thank you therefore!). So I came up with: help.index <- function (pkg,

If I try to build a package with a vignette R CMD build Biobase I see * checking for file 'Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src Error in setwd(pkgname) : cannot change working directory Execution halted This is

Dear R-users, I am going through the last steps of package prep before submission to CRAN and I have the following problem. My package contains a single vignette written in optimbase.Rnw and that in stored in /inst/doc. optimbase.Rnw contains multiple \input{} statements that refer to .tex files stored in /inst/latex.ref/, e.g.: \input{../latex.ref/optimbase-package.tex} When I compile my Rnw

A vignette in <pkg>/inst/doc with \documentclass[]{article} \begin{document} <<test>>= try(stop('err')) @ \end{document} produces an error with R CMD build <pkg>: ... ** building package indices ... * DONE (testPkg) * creating vignettes ... ERROR Error in try(stop("err")) : err This is not seen with Sweave alone. > sessionInfo() R version 2.5.0

A package uses VignetteEngine: knitr; the package itself does not Suggests: knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R CMD check fails indicating that a package required for checking is not declared. Is it really the intention that the original package duplicate Suggests: knitr? This is only with a recent R. In detail, with $ Rdev --version|head -3 R Under

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?: *

Hello R-developers! I am creating a package (using devtools and RStudio) and I would like to split my vignette into multiple Rnw-files. As an example I tried the code from: https://support.rstudio.com/hc/en-us/articles/200486298 (--> Working with multiple Rnw files) The Rnw-files work fine with "Complie pdf" in RStudio as well as with Sweave("Master.Rnw"). But, if I try

Dear list, we have a markdown vignette for our package in vignette/vignette.md This is not visible from within R with the vignette(package = "mypackage") command. I assume the reason is that the vignette function only shows PDF vignettes. Is there any way to circumvent this and display markdown vignettes directly from within R? I tried to seek the answer from R archives and search

Dear R-devels, We have encountered a problem concerning a dead lock in the dependency graph: We have two packages A1 and A2 where A2 extends A1. We have one package vignette for both packages, but which should be included into package A1. So in the "suggests" field of the DESCRIPTION file of A1 we suggest A2 to be able to produce the vignette at build/install time. On the other hand

Hi all, I was trying to create some vignette files for my newly developed package, however wondering whether there could be any simpler way to do so. In writing R extension it is advised to go through Sweave route, however I have already got a big pdf file and want to use this as package vignette. So far I have manually created the inst/doc folder in the main package skeleton, and put that file

Trying to Stangle / Sweave a file $ cat vignette.Rnw %\VignetteEngine{knitr} \documentclass{article} \begin{document} \end{document} results in a misleading error message: ~/tmp$ R CMD Stangle vignette.Rnw Error: Vignette engine package not specified Execution halted when what is missing is the full specification knitr::knitr; 'vignette engine package and function not specified' ?

[Env: R 2.12.2, WinXp] In a vignette for the vcdExtra package, I had a text file, tv.dat under data/, that I used in the vignette as <<tv1,results=verbatim>>= tv.data<-read.table(system.file("data","tv.dat",package="vcdExtra")) head(tv.data,5) @ I was told that this now generates a warning for non-Rdata files in R CMD check. But I'm now

On 09/12/2014, 10:36 PM, Yihui Xie wrote: > I took a look at the R source and I realized that the encoding was > actually never passed to the vignette engine: > https://github.com/wch/r-source/blob/e721ef5f4/src/library/tools/R/Vignettes.R#L507 > Apparently only the file and quiet arguments are passed to the > vignette engine. Did I miss anything? I think it's actually a little

Hello: Clicking "Knit Word" in RStudio 0.99.893 with R 3.3.0, works fine with a vignette with "output: word_document". However, "R CMD build" throws the following error: $ R CMD build pkgW2vignettes * checking for file ?pkgW2vignettes/DESCRIPTION? ... OK * preparing ?pkgW2vignettes?: * checking DESCRIPTION meta-information ... OK * installing the

I think the online order of vignette files are not based on vignette title or filename alphabetically. I am just curious: by what order these vignette files were displayed online so I can make changes accordingly? Thanks, Zhu -----Original Message----- From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] Sent: Friday, March 04, 2016 10:47 AM To: Wang, Zhu; r-devel at r-project.org Subject:

Dear R-users, I am trying to figure out why I cannot print vignettes in my new R installation (R.11 on opensuse 11.2). Apparently, vignette objects are properly created but could not be printed: > z<-vignette('grid') > str(z) List of 3 $ file : chr "/usr/lib/R/library/grid/doc/grid.Snw" $ pdf : chr "/usr/lib/R/library/grid/doc/grid.pdf" $ topic: chr

Full_Name: Chris Evans Version: 2.3.1 OS: Windoze XP Submission from: (NULL) (217.34.100.197) If I give "vignette("introduction")" I get: Error in sprintf(gettext(fmt, domain = domain), ...) : use format %s for character objects vignette() works for some other vignettes and "vignette()" gets me a list of vignettes and shows three with the name