similar to: vignette help

Dear List, I recently stumbled over the possibility and need to specifiy % \VignetteDepends{} in my vignettes. I did not know about this, and I notice that it is not mentioned in the R-extensions manual section "Writing package vignettes". I have some questions with regards to that: - would it be possible to include into the section "Writing package vignettes" some hint

R CMD check gives an error when a vignette entry %\VignetteDepends{} has any extra space at the end. Maybe this is by design, but I found it confusing. Changing the function "vignetteMetaRE" in tools package could solve the problem. I.e. vignetteMetaRE <- function(tag) paste("[[:space:]]*%+[[:space:]]*\\\\Vignette", tag,"\\{([^}]*)\\}", sep = "")

I?m preparing a package (fastR) for submission to CRAN, but the vignette index keeps going AWOL, or at least R CMD check ?as-cran thinks so. I?ve tried several things and gave myself the weekend to think of other things, but I can?t figure it out. Perhaps someone on the list can lend a hand. Here?s one example situation, where I build the index.html file myself and put it in inst/doc/index.html

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

I am having trouble converting the output from Sweave into a valid PDF file. I have created a simple .Rnw file which will become a full vignette at some point, but during the intermediate testing, I got errors from texi2dvi. This is what I have done. 0) Using a Windows Xp system 1) Created a file called GeneSpring.Rnw 2) Convert this to Tex using Sweave("GeneSpring.Rnw") from within R

Late to the show on this release, unfortunately. One of our production packages no longer builds under R-2.15.0 with the following message. ** testing if installed package can be loaded Error: Function found when exporting methods from the namespace 'SuperCurve' which is not S4 generic: 'image' Possibly relevant clues follow: ## From R/AllGenerics.R if

Hi, I have a package for which I'm writing a vignette. The vignette looks fine as indicated by R CMD check. However after installing the package (in my personal R library location) doing vignette('rcdk') says Warning message: vignette 'rcdk' *not* found But I can see the PDF file located under rcdk/doc in the R library directory. The header of the Rnw file is %

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

Hello! I have just discovered a possible bug or lack of my knowledge. The last option is not so uncommon and I decided to ask here before flooding the bugs repository. Say I have a package test with vignette. Moving package directory to some other name, say test2, fails R CMD check with $ R CMD check test2 * checking for working latex ... OK * using log directory

I have built today's R-devel without problem on a fresh installation of debian testing. However, 'make check' fails. In 'tests/Examples/tools-Ex.Rout.fail': > ### * vignetteDepends > > flush(stderr()); flush(stdout()) > > ### Name: vignetteDepends > ### Title: Retrieve Dependency Information for a Vignette > ### Aliases: vignetteDepends > ### Keywords:

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,

Hi R-devel, [Question]: * Is there a KEYWORDS file to lookup 'keywords' to supply the vignette command, '\VignetteKeywords{}'? -or, is the pkg writer free to tag the vignette using any keywords he/she chooses? i.e., free-tagging. Thank you, + Elliot Kleiman __________________________ San Diego State University http://www.sdsu.edu/

>>>>> On Fri, 29 Oct 2004 12:47:46 +0200 (CEST), >>>>> S J Eglen (SJE) wrote: > 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

I am installing R 2.15.1 onto RHEL 6, using gcc 4.7.0 with Intel MKL 10.3.7 and the following environment: export BLAS_LIBS="-Wl,--start-group /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_gf_lp64.a /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_sequential.a /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread" export LAPACK_LIBS="-Wl,--start-group

dears R-users, I'm interested in model selection problem, and i have faced some problems that i would like to ask for help. well, this is a very small example with 4 variable (just one var. is the response - z) with 100 individuals i would like to do a stepwise search, for the "best" model, and a use BIC criteria. I know when I have a lot of variables, let's say 120, I know,

I'm attempting to reflect the information for use with corresponding fields in GUI (in a different package), to provide default values, argname as key for UI label lookups, etc. So I want something much more like the formals of the implementation: { "object", "method": c("median", "vs", "tukey"),

At this point I would just due: formals(body(method)[[2L]]) At some point we need to figure out what to do with this .local() confusion. On Wed, Jan 28, 2015 at 10:07 AM, Roebuck,Paul L <PLRoebuck at mdanderson.org> wrote: > I'm attempting to reflect the information for use with corresponding > fields in GUI (in a different package), to provide default values, > argname

On Jan 28, 2015, at 6:37 PM, Michael Lawrence <lawrence.michael at gene.com> wrote: > At this point I would just due: > > formals(body(method)[[2L]]) > > At some point we need to figure out what to do with this .local() confusion. Agreed, definitely. The current hack is to avoid re-matching arguments on method dispatch, so a fix would need to be fairly deep in the

Can someone show me some code to do normalization by the median of some control genes for the example below? Many Many Thanks in advance This strategy selects a subset of genes (called ?control genes?) and makes the median of their data distribution similar across arrays. ??? ??? id1??? id2??? id3 control1??? 0.8??? 0.7??? 0.6 control2??? 0.6??? 0.2??? 0.4 probe1??? ??? 0.3??? 0.2??? 0.5

Interrogating some (of my own) code in another package. >norm.meth <- getMethod("normalize", "MatrixLike") >message("str(norm.meth)") >str(norm.meth) >message("show(norm.meth at .Data)") >show(norm.meth at .Data) Last show() displays this: function (object, ...) { .local <- function (object, method = c("median",