search for: browsevignettes

...nette() currently produces a listing of available vignettes, but these are not clickable. Since R has a browseURL() function, it seems natural to have a version that produces HTML with clickable links. Here's an attempt at that: source("http://dsarkar.fhcrc.org/R/vignette-browser.R") browseVignettes() browseVignettes(package = "grid") etc. Perhaps some variant of this could be added to R. Comments welcome. -Deepayan

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 refer to any vignettes. The vignette does not appear in the main page for utils in help.start(). I checked the source code for the Sweave vignette, but I don't see anything wrong....

...ter')" cp vignettes/*.pdf* inst/doc Rscript -e "devtools::document()" mkdir inst/extdata/sources_vignettes cp sources_vignettes/*/*.Rnw inst/extdata/sources_vignettes Rscript -e "devtools::build(vignettes = FALSE)" That works fine, the vignettes show up using browseVignettes() after installing the package the normal way. However, after building, the tar.gz contains each pdf corresponding to a vignette twice: once in vignettes and once in inst/doc (which is obvious, when reading the Makefile). >From the reading of "Writing R Extensions" and other material...

...df* inst/doc > Rscript -e "devtools::document()" > mkdir inst/extdata/sources_vignettes > cp sources_vignettes/*/*.Rnw inst/extdata/sources_vignettes > Rscript -e "devtools::build(vignettes = FALSE)" > > That works fine, the vignettes show up using browseVignettes() after > installing the package the normal way. > > However, after building, the tar.gz contains each pdf corresponding to a > vignette twice: once in vignettes and once in inst/doc (which is obvious, > when reading the Makefile). > > From the reading of "Writing R Ext...

...evel. This happened on two independent computers (WinXP Prof. SP3, German) with R-devel compiled from sources svn rev. 48125 resp. 48128 It's the same for my own and also for more prominent packages as well (e.g. grid). The vignettes and the index.html files exist and vignette() as well as browseVignettes() work as expected. I have not found anything about this in NEWS or "Writing R extensions", which says: "At install time an HTML index for all vignettes is automatically created from the \VignetteIndexEntry statements unless a file index.html exists in directory inst/doc. This i...

...========== OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb ======================= Loading required package: Biobase Loading required package: methods Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: gcrma Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from 'package...

...ript -e "devtools::document()" > > mkdir inst/extdata/sources_vignettes > > cp sources_vignettes/*/*.Rnw inst/extdata/sources_vignettes > > Rscript -e "devtools::build(vignettes = FALSE)" > > > > That works fine, the vignettes show up using browseVignettes() after > > installing the package the normal way. > > > > However, after building, the tar.gz contains each pdf corresponding to a > > vignette twice: once in vignettes and once in inst/doc (which is obvious, > > when reading the Makefile). > > > > From t...

Hi, I have a set of genes and its chromosomal physical position in a text file. I want to view those genes in the chromosome using R package GenePlotter. Could any one please tell how to view this. Thanks in advance. Yours sincerely, S.Mahalakshmi [[alternative HTML version deleted]]

...tersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: org.Hs.eg.db Loading required package: DBI Error : .onLoad failed in loadNamespace() for 'hugene10sttranscriptcluster.db', det...

Hi all, Because str uses the generic version of length and names, it's currently very easy to create objects that break str: a <- structure(list(1:5), class = "a") length.a <- function(x) 2L str(a) b <- structure(list(1:5), class = "b") names.b <- function(x) character() str(b) These are obvious toy examples, but it is a real problem if you want to create

...kage. I think that documents under inst/doc are a > bit hard to find if package authors do not create (possibly many) links > to them in Rd files or vignettes. What I'd suggest is that you write a "browseDocs" function that displays them in some nice format (similar to "browseVignettes"). Maybe CRAN would choose to add a new category listing its results, but at a minimum, you could very easily add a vignette called "Other documents" that contains a list of links. It wouldn't be as prominent as "Vignettes" on CRAN, but you could make the display...

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

As a user, I am always annoyed beyond measure that Sweave vignettes precede the code by a command line prompt. It makes running examples by simple copying of the commands from the vignette to the console a pain. I know the idea is that it is clear what is the command, and what is the output, but I'd rather precede the output with some kind of marking. Is there any other solution possible /

Dear folks, Please welcome a newbie both to R and the mailing list :). I am currently working on a sequencing project, and heard about R as well as some of its packages for next gen sequencing, and decided to give it a try. Starting with ShortRead, I found a document (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention

On 01/11/2020 2:57 p.m., Dirk Eddelbuettel wrote: > > The closest to a canonical reference for a static vignette is the basic blog > post by Mark at > > https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ > > which I follow in a number of packages. > > Back to the original point by Alexandre: No, I do _not_ think we can do >

Hi, I'm very confused about R structures and the methods to go with them. I'm using R for microarray analysis with Bioconductors. Suppose without reading the documentations, what's the best way to explore a data structure when you know nothing about it? I am currently using is() / class() to see what the object is. str() / attributes() to probe inside the object, and

Hi, I am using "*Maanova* package" to do anova. I have created *datafile* with probeID as the first column, which is a tab limited text file and also created *designfile*. I have created *readma object* which is named as abf1. >From that readma object, i have to create data object by using *createData*function and also i hav to create model object by using *makemodel* function,

A new problem has cropped up with compiling vignettes for my package BayesFactor. I'm not sure when it started, but I can tell you it didn't occur on R 2.15.3, and it does on 3.0.0 RC (2013-03-31 r62463) (session info is at the bottom of this message). I have defined methods for which.min and which.max for a class (I've defined both S3 and S4 methods for the class

...n as.octmode() to create objects such as file permissions. o as.POSIXlt() is now generic, and it and as.POSIXct() gain a '...' argument. The character/factor methods now accept a 'format' argument (analogous to that for as.Date). o New function browseVignettes() lists available vignettes in an HTML browser with links to PDF, Rnw, and R files. o There are new capabilities "aqua" (for the AQUA GUI and quartz() device on Mac OS X) and "cairo" (for cairo-based graphics devices). o New function checkNE...

...n as.octmode() to create objects such as file permissions. o as.POSIXlt() is now generic, and it and as.POSIXct() gain a '...' argument. The character/factor methods now accept a 'format' argument (analogous to that for as.Date). o New function browseVignettes() lists available vignettes in an HTML browser with links to PDF, Rnw, and R files. o There are new capabilities "aqua" (for the AQUA GUI and quartz() device on Mac OS X) and "cairo" (for cairo-based graphics devices). o New function checkNE...