similar to: NAMESPACE/DESCRIPTION and imports

Dear cateGOry experts, hyperGTest documentation states that YEAST cannot be used as 'annotation' when evaluating gene ontology representation status for a given set of 'geneIds'. Because I am using a custom print I believe I need to create my own data package to use as the annotation file for 'annotation'. Can someone please describe how to make a data package that will

Hi, I was wondering if there's a way in R to open a web browser (such as Internet Explorer, or Firefox or whatever). I'm doing some analyses that have associated urls, and it would be nice to have the ability to directly open the relevant page from within R. I was looking at the help for 'url' and I can see I can probably access the information I need and display it in my

Hello list, I am writing a package which builds on a function ("foo") of another package. I only need that particular function. What is the state of the art to do this? Do I need a NAMESPACE file in my package? Currently I still don't have one. Or can I do this with the Imports field in my DESCRIPTION file? Reading chapter 1 of the "Writing R Extensions" manual I do

On Solaris when my package is built, I get the following result: creating vignettes ...Segmentation Fault - core dumped OK My question isn't why I get a segfault, but why does build return an OK after such an inauspicious event? Is build only supposed to error out if something more central to the package is off? R CMD check does issue a warning that the vignette is missing, so maybe that

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

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

I just built R-devel from source on OS X (Tiger), using the subversion sources. Running ./tools/rsync-recommended didn't download rcompgen. I checked http://cran.r-project/src/contrib/2.7.0/Recommended and indeed, this package is not there. If I try to install using install.packages I get > install.packages("rcompgen", type="source") --- Please select a CRAN

> R.version.string [1] "R version 2.1.0, 2005-03-17" I don't see anything in either https://svn.r-project.org/R/trunk/NEWS or in the Changes file for R-2.1.0 about changes in package.skeleton() (nor in the help page), but when I run this function, all the .Rd files produced are of the data format even if all I have in my .GlobalEnv are functions. A trivial example is to run the

Hi all, Most of the analyses I do are short little once-and-done type things that are easily encapsulated in a .Rnw file. However, I sometimes end up with projects that take an extended amount of time. Usually these projects are not easily encapsulated in an .Rnw file, so I have been using a single .R file with lots of comments. The problem with this approach is keeping track of what you have

Dear all, It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'. Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj'

Hi, I am a bit unsure about using imports in packages and have a few questions. I'm sure the answer to some of these is 'it depends', but I'm interested in what others think and 'best practices' when this is the case. 1) If I use an import or importFrom declaration in a NAMESPACE, should I also qualify the package in calls to the imported function (e.g.

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" section 1.6.6 of 'Writing R Extensions' says Note that exporting methods on a generic in the namespace will also export the generic, and exporting a generic in the namespace will also export its methods. and Note that importMethodsFrom will also import any generics defined in

If one wants to unload compiled code for a package containing a namespace, my understanding is that .onUnload() should be used, with a call to library.dynam.unload(). This is used in e.g., the stats and methods packages, but it appears to me that the compiled code is not being unloaded when the package is detached(). Am I misunderstanding something? Best, Jim > search() [1]

I am cleaning up the rms package to not export functions not to be called directly by users. rms uses generic functions defined in other packages. For example there is a latex method in the Hmisc package, and rms has a latex method for objects of class "anova.rms" so there are anova.rms and latex.anova.rms functions in rms. I use:

Hi, I have a package that contains two vignettes that both use saved objects in the examples directory of the package. With previous versions of R I could have a code chunk in the vignette like this: <<echo=false>>= load("../examples/somedata.Rdata") @ followed by a code chunk like <<eval=false>>= foo <- bar("data") @ that simulated the actual

The function knn.cv in the class package doesn't have error checking to ensure that the length of the classlabel argument is equal to the number of rows in the test set. If the classlabel is short, the result is often a segfault. > library(class) > dat <- matrix(rnorm(1000), nrow=10) > cl <- c(rep(1,5), rep(2,5)) > cl2 <- c(rep(1,5), rep(2,4)) > knn.cv(dat, cl) [1] 2

PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A)

I have 2GB installed on my windows XP box running R 1.9.0, and after performing a prune.tree(intree,newdata), I get an out of memory error within R, but it says the maximum allowed is 1024gb (1/2 of what I have!) Can R not use more than 1GB on an XP box? I noticed I had ~600mb left over after R conked out, so clearly I had more memory... What about virtual memory? --j -- Jonathan Greenberg

Hi dear R-listers, I'm trying to fit a 3-level model using lme in R. My sample size is about 2965 and 3 factors: year (5 levels), ssize (4 levels), condition (2 levels). When I issue the following command: > lme(var~year*ssize*condition,random=~ssize+condition|subject,data=smp,method ="ML") I got the following error: Error in logLik.lmeStructInt(lmeSt, lmePars) :

Why does stop("we are done") print "Error in eval.with.vis(expr, envir, enclos) :" ? It would seem to me that a plain stop() is not an error, and that it would make more sense to have an error() function that is different from a stop(). Is there a rationale here that I am missing? sincerely, /iaw