similar to: Creating a vignette which depends on a non-distributable file

On 05/14/2015 04:33 PM, Henrik Bengtsson wrote: > On May 14, 2015 15:04, "January Weiner" <january.weiner at gmail.com> wrote: >> >> Dear all, >> >> I am writing a vignette that requires a file which I am not allowed to >> distribute, but which the user can easily download manually. Moreover, it >> is not possible to download this file

On May 14, 2015 15:04, "January Weiner" <january.weiner at gmail.com> wrote: > > Dear all, > > I am writing a vignette that requires a file which I am not allowed to > distribute, but which the user can easily download manually. Moreover, it > is not possible to download this file automatically from R: downloading > requires a (free) registration that seems to

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 /

Dear R gurus I?m trying to use the GSCA package to a series of microarray data (prostate cancer normal vs tumor (29 vs 29 paired)) but I?m running into some problems. I have a matrix (named /data_final/) with 11k rows(genes) and 60 cols (58 samples (29N vs 29T), GO IDs, KEGG IDs). I also have a separate vector GS with the GO IDs mapped to genes (no duplicate genes but multiple IDs per gene like

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

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

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

Dear all, In my package I have a computational expensive Rnw file which can't pass R CMD check. Therefore I set eval=FALSE in the Rnw file. But I would like to have the pdf vignette generated by the Rnw file with eval=TRUE. It seems to me a static pdf vignette is an option. Any suggestions on this? Thanks, Zhu Wang **Connecticut Children's Confidentiality Notice** This e-mail

I am trying to find a simple R guide that explain what a vignette is but so far I didnt make any progress. I tried to search inside R's built in help.start() but it only returns results how to see vignettes. So could you please tell me what a vignette is and if you can also could you give some simple guide that I can always use to read about these things? Best Regards Alex

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

In ?Sweave, it refers to Sweave User Manual. In the doc folder of utils package, I see "Sweave.pdf". However, I can't find it from within R > vignette("Sweave User Manual") Warning message: vignette ?Sweave User Manual? not found > browseVignettes("utils") No vignettes found by browseVignettes("utils") > library(help=utils) does not

Hi, this is tangentially related to the recent discussion on vignettes. vignette() currently produces a listing of available vignettes, but these are not clickable. Since R has a browseURL() function, it seems natural to have a version that produces HTML with clickable links. Here's an attempt at that: source("http://dsarkar.fhcrc.org/R/vignette-browser.R") browseVignettes()

I recently wrote a vignette, with the following at the top of the .Rnw file: %%\VignetteIndexEntry{How to use look up tables for h() functions} %%\VignetteDepends{sjedmin, spatstat} Using vExplorer() on this function, I got an error from this part of getVigInfo(): lines <- grep("^%[[:space:]]*\\\\Vignette", file) if (length(lines) == 0) stop("File ", vig,

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:

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

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

Dear colleagues, I am having issues trying to build a R package I recently wrote. I am using R 2.14.0 and my package depends on another package called aod. Running: R CMD Sweave vignette.Rnw is perfectly fine and the vignette compiles properly. but when I use R CMD build mypackage to build the tar.gz I get the following error: * installing the package to re-build vignettes * creating

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, I am trying to run "RCMD check" on a package. It performs OK, with the exception of a single warning: * checking package vignettes in 'inst/doc' ... WARNING Package vignette(s) without corresponding PDF: AnnotationFuncsUserguide.Rnw As I understand the problem, the vignette is not built. However, I have no problems in doing so manually. How do I fix this problem? I