Displaying 20 results from an estimated 30000 matches similar to: "Requests for vignette clarification (re: Writing R Extensions)"
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
2002 Oct 30
4
Sweave in packages
Dear R folks,
One of the fantastic new tools in R is `Sweave'. I have tested it so much that I
know it works and produces fine documentation, and with (GNU) Emacs/ESS it is
nice to work with, too. I started to have a look at including some Swoven (is
that a strong verb?) documentation with my R package, but it seems that there is
no model to copy among those packages that I have installed in
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
2016 Jan 12
1
Small inaccuracy in the Writing R Extensions manual
G'day Duncan,
On Tue, 12 Jan 2016 07:32:05 -0500
Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> On 11/01/2016 11:59 PM, Berwin A Turlach wrote:
> > G'day all,
> >
> > In Chapter 1.4 (Writing package vignettes) the Writing R Extensions
> > manual states:
> >
> > By default @code{R CMD build} will run @code{Sweave} on all
> >
2013 Sep 17
2
processing of /vignettes and /inst/doc
It is stated in R-exts that Sweave files (.Rnw) are either processed in
/vignettes or /inst/doc, not both. Furthermore, it is stated that external
manuals and other files in /inst/doc will be installed.
This behaviour has been used to deal with the situation where a package has
two "vignettes", one that is easily processed and one that has a long
running time. This could be done by
2011 Nov 07
3
CRAN: How to list a non-Sweave doc under "Vignettes:" on package page?
Hi,
is it possible to have non-Sweave vignettes(*) in inst/doc/ be listed
under 'Downloads' on CRAN package pages? For instance, in my R.rsp
package I have a inst/doc/report.pdf (part of the source *.tar.gz)
that is not detected/listed. The PDF is not based on a Sweave
vignette but an *.tex.rsp vignette that is dynamically created via
inst/doc/Makefile. It is listed
(*) BTW, can the
2012 Jun 06
1
stumped on re-building package vignette
[Env: Win Xp / StatET 2.0 / R 2.15.0]
In my heplots package I extended the HE-examples.Rnw vignette under
inst/doc. The package passes R CMD check
on my machine:
* using log directory 'C:/eclipse-3.7/heplots.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: i386-pc-mingw32 (32-bit)
...
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files
2013 Oct 13
1
Compatibility with R 2.15.x: Makefile for (non-Sweave) vignettes in vignettes/?
In R 3.1.0 (~April 2014), support for vignettes in inst/doc/ will go
away (and probably much sooner for CRAN submission), e.g.
checking for old-style vignette sources ... NOTE
Vignette sources only in ?inst/doc?:
?R.devices-overview.tex.rsp?
A ?vignettes? directory is required as from R 3.1.0
and these will not be indexed nor checked
I've been sticking with inst/doc/ for backward compatible
2008 Jan 21
1
Adding an Sweave Vignette to a package
I'm finalizing development of a package that will include a vignette.
Without the vignette, the package builds fine with no warnings and is
ready for distribution. Now, I am following the directions for
developing vignettes "Sweave, Part II: Package Vignettes" by Friedrich
Leisch.
I am using a windows XP machine (other session info below). Here is what
I have done.
1) I add the
2012 Sep 18
2
problem with vignettes when S4 classes in packages overlap
( A similar problem is also reported by Sebastian P. Luque with
library(maptools)
library(trip)
in the vignette as below ).
I am writing a vignette which loads RMySQL and RPostgreSQL. This
produces the warning:
Loading required package: DBI
Warning in .simpleDuplicateClass(def, prev) :
A specification for class ?dbObjectId? in package ?RPostgreSQL? seems
equivalent to one from package
2012 Apr 11
2
Vignette questions
Context: R2.15-0 on Ubuntu.
1. I get a WARNING from CMD check for "Package vignette(s) without
corresponding PDF:
In this case the vignettes directory had both the pdf and Rnw; do I
need to move the pdf to inst/doc?
I'm reluctant to add the pdf to the svn source on Rforge, per the
usual rule that a code management system should not have both a primary
source and a object
2013 Apr 21
2
vignettes: problems with PDF compaction
[Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET]
Each time I update my heplots package, I get warnings from R CMD check
on R-Forge,
* checking sizes of PDF files under ?inst/doc? ... WARNING
?gs+qpdf? made some significant size reductions:
compacted ?HE-examples.pdf? from 739Kb to 366Kb
and upon submission to CRAN, a message from maintainers:
On CRAN now: but again there were warnings
2013 Feb 11
1
Avoid re-building a vignette
I once knew the answer to this, but can't find where I found it.
Say I have a vignette that I don't want R to automatically rebuild, perhaps it uses some
data I can't share or takes too long to run or whatever. Say it is
mypackage/vignettes/charlie.Rnw
It can create the pdf from an R session that actually has the data, place that result in
inst/doc/charlie.pdf, then run
R
2016 Jan 12
3
Small inaccuracy in the Writing R Extensions manual
G'day all,
In Chapter 1.4 (Writing package vignettes) the Writing R Extensions
manual states:
By default @code{R CMD build} will run @code{Sweave} on all
Sweave vignette source files in @file{vignettes}. If
@file{Makefile} is found in the vignette source directory, then
@code{R CMD build} will try to run @command{make} after the
@code{Sweave} runs, otherwise @code{texi2pdf} is run on
2011 Mar 30
1
R CMD build processes inst/doc/Makefile only if there are vignette files?
Hi,
in Section 'Writing package vignettes' of 'Writing R Extensions' it says:
"Whenever a Makefile is found, then R CMD build will try to run make
after the Sweave runs, so PDF manuals can be created from arbitrary
source formats (plain LaTeX files, ...). [...] Note that the make step
is executed even if there are no files in Sweave format, [...]".
In my package,
2014 Feb 20
1
Where to put package vignettes
Dear R-devel list,
My name is Guillermo Vinu?. I have created an R package that includes a
vignette. Earlier on, to test my package, I tried to install it both in
Linux and Windows and it worked. My vignette was in /inst/doc.
Now, I have finished for good and before submitting my package to CRAN
I've tried to install it again first in Linux and then in Windows (I
removed that first
2009 May 10
2
Vignettes with missing or empty \VignetteIndexEntry:
Hi,
I have a problem when checking the package 'probdistr' (on probability
distributions).
I got this warning
* checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
[1] "probdistr-chi" "probdistr-contextra" "probdistr-discrete"
[4] "probdistr-discrextra" "probdistr-exp"
2010 Aug 13
2
cacheSweave / pgfSweave driver for package vignette
Dear list,
I wish to use a specific driver to process an sweave document in the
inst/doc directory of a package. Specifically, I would like to use
either cacheSweave or pgfSweave to speed up the creation of the
vignette which requires lengthy computations. The same request would
also apply to the highlight driver, to provide syntax highlighting of
R chunks.
In "writing R extensions" I
2010 Aug 13
2
cacheSweave / pgfSweave driver for package vignette
Dear list,
I wish to use a specific driver to process an sweave document in the
inst/doc directory of a package. Specifically, I would like to use
either cacheSweave or pgfSweave to speed up the creation of the
vignette which requires lengthy computations. The same request would
also apply to the highlight driver, to provide syntax highlighting of
R chunks.
In "writing R extensions" I
2015 May 14
2
Creating a vignette which depends on a non-distributable file
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 work only through a browser.
(I'm talking here about the MSigDB from the Broad Institute,