search for: weave

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: \documentclass{article} \begin{document} Assign 1 to x: \Sexpr{x <- 1} <<>>= x + 1 @ \end{document} That is because the inline R...

I thought some of you might be amused by this. In my non-work time, I'm an avid weaver and teacher of weaving. I'm working on a project involving creating many detailed weaving patterns, so I wrote R code to automate it. Details here: http://stringpage.com/blog/?p=822 If the overlap between R users and avid tablet weavers turns out to be >> 1, I'll polish it up and t...

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...

...ette-related errors with recent versions of R-3.0.0 alpha. First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ?BitSeq.Rnw' failed with diagnostics: Failed to locate the ?weave? output file (by engine ?utils::Sweave?) for vignette with name ?BitSeq?. The following files exists in directory ?.?: ?data-C0.est?, ?data-C1.est?, ?data-c0b0.prob?, ?data-c0b0.rpkm?, ?data-c0b0.sam?, ?data-c0b0.thetaMeans?, ?data-c0b1.rpkm?, ?data-c1b0.rpkm?, ?data-c1b1.rpkm?, ?data.estVar?, ?dat...

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...

...about reproducibility (e.g., when the sessionInfo() of a later vignette reflects packages used in earlier vignettes). I believe the relevant code is at src/library/tools/R/Vignettes.R:505 output <- tryCatch({ ## FIXME: run this in a separate process engine$weave(file, quiet = quiet) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine) }, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditi...

..., patterns)}) > 7: split_file(lines = text) > 8: process_file(text, output) > 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding) > 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv()) > 11: vweave_rmarkdown(...) > 12: engine$weave(file, quiet = quiet, encoding = enc) > 13: doTryCatch(return(expr), name, parentenv, handler) > 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 15: tryCatchList(expr, classes, parentenv, handlers) > 16: tryCatch({ engine$w...

I have two questions about packaging up code. 1) Weave/tangle advisable? In the course of extending some C code already in S, I had to work out the underlying math. It seems to me useful to keep this information with the code, using Knuth's tangle/weave type tools. I know there is some support for this in R code, but my question is about the wisd...

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,

...ohn Fox's car package). And the latter are implemented in the function vcovHAC(). This implements sandwich-type estimators in a rather flexible way, allowing for user-defined weights or weight functions. It builds on some of the functionality which was before available in Thomas Lumley's weave package (not on CRAN). In particular it makes available the class of WEAVE estimators introduced by Lumley & Heagerty (1999) in the function weave() which is a convenience interface to vcovHAC(). Furthermore, it implements the class of kernel HAC estimators with automatic bandwidth-selection of...

...ohn Fox's car package). And the latter are implemented in the function vcovHAC(). This implements sandwich-type estimators in a rather flexible way, allowing for user-defined weights or weight functions. It builds on some of the functionality which was before available in Thomas Lumley's weave package (not on CRAN). In particular it makes available the class of WEAVE estimators introduced by Lumley & Heagerty (1999) in the function weave() which is a convenience interface to vcovHAC(). Furthermore, it implements the class of kernel HAC estimators with automatic bandwidth-selection of...

...R code, but *not* code fragments. You can *not* intersperse comments in, say, a function body, or local() environment this way : when Sweaving, *R* complains of an incomplete source (makes noise about an unexpected end of input at the end of Chunk1, IIRC, and never sees Chunk2). I hoped that Sweave's "alternative" syntax could offer a way out : no such luck. There seems to be no way to delay R evaluation of a R chunk passed by Sweave ; at least, the "eval=FALSE" option of chunk declaration is not sufficient for that. Am I missing something in the Sweave nd odfWeve...

...c) } else parse_inline(g, patterns)}) 7: split_file(lines = text) 8: process_file(text, output) 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding) 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv()) 11: vweave_rmarkdown(...) 12: engine$weave(file, quiet = quiet, encoding = enc) 13: doTryCatch(return(expr), name, parentenv, handler) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: tryCatchList(expr, classes, parentenv, handlers) 16: tryCatch({ engine$weave(file, quiet = quiet, enco...

Hello, I want to use seq with multiple from values and am getting unexpected (to me) behavior. I'm wondering if this behavior is intentional or not. > seq(2, by=3, length.out=4) [1] 2 5 8 11 > seq(3, by=3, length.out=4) [1] 3 6 9 12 Now if I want the combined sequence, I thought I could pass in c(2,3), and I get: > seq(c(2,3), by=3, length.out=8) [1] 2 6 8 12 14 18 20 24

Hi, With the following Sweave minimal file: ---<--------------------cut here---------------start------------------->--- \documentclass{article} \usepackage{Sweave} \begin{document} <<binom-sim>>= thetas <- seq(0, 1, by=0.001) prior <- rep(1, length(thetas)) / length(thetas) lik <- dbinom(1, 1, th...

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 Statistician Epidemiology Steno Diabetes Center A/S Niels Steensens Vej 2-4 DK-2820...

...): [1] digest_0.6.8 htmltools_0.2.6 I also made sure to remove all instances of rmarkdown before installing the older version. However, R CMD build nls14 still gives lots of errors (these are related to content in the vignette source and are, I believe, consequent on the warning about engine$weave). The warning still refers to the later version of pandoc which Ubuntu 14.04 repos don't yet have. My current guess is some mismatch in the software infrastructure. I have another machine with R 3.1.2 and rmarkdown_0.3.3 that manages to build the package without complaint, but it would be goo...

...le(lines = text) >> 8: process_file(text, output) >> 9: knitr::knit(knit_input, knit_output, envir = envir, quiet = >> quiet, encoding = encoding) >> 10: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir >> = globalenv()) >> 11: vweave_rmarkdown(...) >> 12: engine$weave(file, quiet = quiet, encoding = enc) >> 13: doTryCatch(return(expr), name, parentenv, handler) >> 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 15: tryCatchList(expr, classes, parentenv, handlers) >> 16: tr...

...today) before sending a new release to CRAN. It has a few false positives which I then follow up on.? (Mostly packages with as-yet-incomplete tests in their inst directory). ?Issue: testInstalledPackage("mets")? generates an? "Error in checkVignettes(pkg, lib.loc, latex = FALSE, weave = TRUE)" message, which stops my script.? The source code for that package passes R CMD check. I can easily work around this in the short term by adding mets to my do-not-check list. Footnote: the newer "check_packages_in_dir" routine doesn't work for me.?? The biggest reason...

I've written some "rough" functions for base conversion and digit interweaving (as in x=135, y=246, interwoven=123456) which are ok for a small number of conversions or weaves, but, to be able to handle a large number of conversions or weaves, I'm hoping that some faster code already exists (ideally calling C or FORTRAN). Any suggestions for going base10 to base2, base2 to base4, or digit interweaving would be appreciated. regards, Richard Remington -.-.-.-.-.-.-...