Displaying 20 results from an estimated 4000 matches similar to: "file.system() in packages"
2009 Sep 08
1
makefile for sweave
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
2012 Aug 06
1
bibtex::read.bib -- extracting bibentry keys
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?
2011 Dec 16
2
R package BibTex entries: looking for a more general solution
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
2014 Mar 14
1
Problems building package vignette: Sweave requires multiple passes to build document.
Dear R-devel,
Question:
How can I get Sweave to recognize that the \thebibliography section
is already created and generate the vignette pdf with a single pass? Or
is there a way to let R CMD build know that Sweave needs to be run twice?
If (1) is not possible, any suggestions how to auto-generate a
crude generic bibtex .bib file from my existing document?
Background:
I maintain
2010 Nov 03
3
R package BibTex entries: looking for a more general solution
== 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
2008 Oct 23
1
Automating citations in Sweave
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
2008 Oct 28
1
Sweave, Bibtex, package references
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
2012 Nov 22
2
BibTeX entries in CITATION file
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
2002 Jul 17
1
editing Sweave files in xemacs with ess (noweb), auctex and reftex
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
2019 May 29
3
Making a package CITATION file from BibTeX
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
2009 Dec 11
1
Creating bibtex file of all installed packages?
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),
2013 Mar 13
1
Failed to locate 'weave' output file / vignette product does not have a known filename extension
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
2015 Jan 25
1
R CMD check message: "The following files should probably not be installed"
I am doing [R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet?; Platform: x86_64-apple-darwin10.8.0 (64-bit)]
> R CMD build DAAGviz
> R CMD check DAAGviz_1.0.3.tar.gz
Without a .Rinstignore file, I get:
<<<
The following files should probably not be installed:
?figs10.pdf?, ?figs11.pdf?, ?figs12.pdf?, ?figs13.pdf?, ?figs14.pdf?,
?figs5.pdf?, ?figs6.pdf?, ?figs9.pdf?
2019 May 29
0
Making a package CITATION file from BibTeX
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
2009 Dec 11
12
Literature analysis
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
2004 Feb 26
2
Sweave and Xemacs on Windows2000?
Hallo!
Trying to configure Xemacs to work with .snw files on windows 2000. Tried to do it how it is described in the FAQ for Sweaves.
When starting xemacs with and Snw file
*ESS* buffer contains hundrets of lines and the few last ones.
(ess-loop-timeout . 500000) (inferior-ess-primary-prompt . ^) (inferior-ess-secondary-prompt . ^) (comint-use-prompt-regexp-instead-of-fields . t)
2003 Apr 23
1
Setting up Xemacs + Sweave
Dear list,
I have tried to setup my Xemacs for use with Sweave, which I indend to learn.
I have followed the instructions in the Sweave FAQ, that is to say, I put
(defun Rnw-mode ()
(require 'ess-noweb)
(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
2003 Nov 13
1
Can't get Sweave syntax highlighting with Emacs
I can't get Emacs to automatically do syntax highlighting of
Sweave files. I have followed Friedrich's suggestion for code
to insert into my .emacs file. The complete section from my .emacs
file is given below. When I load a *.Snw file, font is white until I press
M-x, then the first code and document chunks get highlighted, but not
the rest of the file. Latex and Noweb menus are
2007 Feb 08
4
NEWBIE: @BOOK help?
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 =
2017 Sep 08
0
post_processor in rmarkdown not working
That is strange. Another function in the same package
(INBOmd::inbo_rapport) uses the same trick. I actually started by copying
the post_processor() from that function. INBOmd::inbo_rapport() works both
with and without BibTex. Working examples are source/inbo_rapport and
source/inbo_rapport_basic from https://github.com/inbo/inbomd_examples.
Note that you need some extra work after installing