similar to: Problems building package vignette: Sweave requires multiple passes to build document.

I added a bibliographic reference to one of my .Rnw documents, to wit: \begin{thebibliography}{9} \bibitem{Jose} Jos{\'{e}} C. Pinheiro and Douglas M. Bates, \emph{Mixed-Effects Models in S and S-PLUS}, Springer, 2000. \end{thebibliography} just before the \end{document}. When I run Sweave on the result these lines disappear without a trace. Is this intentional? Subquestion: is

Back in 2010 I raised this issue, and there was some discussion, https://stat.ethz.ch/pipermail/r-devel/2010-November/058987.html The goal, then, as now is to have a way to produce a bibtex-clean .bib file (i.e., not requiring manual editing except in unusual circumstances) reflecting installed packages for use in writing where one often needs/wants to cite all packages used in a given

== Summary == * Problem: BibTeX entries extracted from R packages via citation() require too much manual editing to be of general use. * Proposal: Date: fields should be made mandatory in package DESCRIPTION files, perhaps beginning with warnings from R CMD check * Proposal: Package authors should be encouraged to use a (new) Contributors: field in the DESCRIPTION file rather than packing all

Dear all, Is there an elegant way to add citations of packages when using Sweave? Ideally I'd like a function which creates a Bibtex-file with the packagenames as keys. The idea is to use \cite{packagename} or \cite{R} in LaTeX. I know you can get the Bibtex entry with toBibtex(citation("packagename")). But after updating R or a package one needs to update the bib-file too. When

I have two versions of a bibtex database which have gotten badly out of sync. I need to find find all the entries in bib2 which are not contained in bib1, according to their bibtex keys. But I can't figure out how to extract a list of the bibentry keys in these databases. A minor question: Is there someway to prevent read.bib from ignoring entries that do not contain all required fields?

Hello. R-devel, r61697. I am having difficulty interpreting section 1.4 "Writing package vignettes" of the R-exts manual. Specifically, I want to use system.file() in some of my packages to locate a bib file, uncertainty.bib, which is part of the emulator package. I only want to maintain a single .bib file. R-exts says: "All other files needed to re-make the vignette PDFs (such

Hello, I have the following makefile. The problem is that the bibliography doesn t work. Any help would be appreciated! I really don t don t what to do..:-( # The sources of the report (tex, Rnw and other files (e.g. bib, idx)) TEX_CMPS = Report problem RNW_CMPS = prop1 prop2 ExeExps OTHER = Report.bib # The name of the report to produce all: Report.pdf code: $(RNW_CMPS:=.R) clean: rm

Dear all, I'm a big fan and happy user of the Sweave package for routine reporting. From inside a .Rnw script, I'd like to produce the references in bibtex format for each package loaded in the environment, write them in a .bib file and load them back from the \bibliography{bibliography} statement. Is this feasible? Any help would be greatly appreciated! Thanks in advance, Paolo

Dear Colleagues, I would like to provide a CITATION file for my package nat.nblast [1]. I have the correct citation in BibTeX format [2]. How can I convert this BibTeX to the format needed by R for a package CITATION file (I have a lot of other packages needing citations ...). I think what I need is the opposite of RefManageR::toBiblatex [3]. This seems like it should be a common need, so I

Dear List, While trying to define a customised CITATION file for a package, following R-exts, I realised that if I use only one 'citEntry' I got both a text description and a BibTex entry for the package, as for the 'nlme' package: -------------------------- citation('nlme') To cite package 'nlme' in publications use: Jose Pinheiro, Douglas Bates, Saikat

Hello, I'm seeing three different vignette-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

On Thu, 30 May 2019, Dr Gregory Jefferis wrote: > Dear Colleagues, > > I would like to provide a CITATION file for my package nat.nblast [1]. > > I have the correct citation in BibTeX format [2]. How can I convert this > BibTeX to the format needed by R for a package CITATION file (I have a > lot of other packages needing citations ...). (1) You can use read.bib() from the

Dear all, i am new in R. I am writing a review paper about batteries. However, i am interested in analyzing all the papers by keywords, author, references and year. This could be done by "refviz" a software, which is only running on windows machines and which is not free. So my question to you is, is it somehow possible to write a script that can do all of this work? And if yes, with

Dear R-help, I'm using prop.test() to compute a confidence interval for a proportion under R version 2.4.1, as in: prop.test(x = 340, n = 400)$conf [1] 0.8103309 0.8827749 I have two questions: 1) from the source code my understanding is that the confidence interval is computed according to Wilson, E.B. (1927) Probable inference, the law of succession, and statistical inference. J. Am.

Hi is there an easy and fast way, to generate a BibTeX file of all installed / loaded packages and R? I know about toBibtex(citation()) to extract the BibTeX for a single package, but how can I generate a file containg citations for all installed / loaded packages? Cheers, Rainer -- NEW GERMAN FAX NUMBER!!! Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT),

In Henric's recent post, he included this output: @BOOK{R:Harrell:2001, AUTHOR = {Frank E. Harrell}, TITLE = {Regression Modeling Strategies, with Applications to Linear Models, Survival Analysis and Logistic Regression}, PUBLISHER = {Springer}, YEAR = 2001, NOTE = {ISBN 0-387-95232-2}, URL =

I am having some trouble getting reftex, in particular the bibtex related features, to work properly in xemacs when editing text in Sweave files. I have added (defun Rnw-mode () (noweb-mode) (if (fboundp 'R-mode) (setq noweb-default-code-mode 'R-mode))) (add-to-list 'auto-mode-alist '("\\.Rnw\\'" . Rnw-mode)) (add-to-list 'auto-mode-alist

utils::citation() offers the option auto=(NULL|TRUE) to obtain the citations for a package from the package DESCRIPTION file or a CITATION file, as described below: |auto| a logical indicating whether the default citation auto-generated from the package 'DESCRIPTION' metadata should be used or not, or |NULL| (default), indicating that a 'CITATION' file is used if it exists, or

In fact my first vignette full stop. I am intending to use Sweave. I have read the Sweave documentation and section 1.4 of the extensions manual and apart from (a) do not use split = TRUE (b) and include all the source components, there does not seem to be anything CRAN specific. 1 - Am I missing some other documentation? 2 - If I use a package from CTAN would that be considered within the

I apologize that these questions are stupid and literal. I write to ask for clarification of comments in the R extensions manual about vignettes. I'm not great at LaTeX, but I'm not a complete novice either, and some of the comments are puzzling to me. 1. I'm stumbling over this line: "Make sure all files needed to run the R code in the vignette (data sets, ...) are accessible