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In "Writing R Extensions" (1.7.0 (2003-04-16). ISBN 3-901167-54-4) under the section "Writing R help files" and the subsection "Cross-references" the usage of \link is currently a little bit unclear: "There are optional arguments specified as \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg with topic (file?) foo and bar respectively." I

Hi, with R v1.7.1 (=I don't recall I saw it before) I noticed that R CMD INSTALL sometimes generates nonsense information, e.g. "Bundle: NA", even if there was a correct DESCRIPTION file too. I turns out that it happens when a DESCRIPTION.in has empty lines at the end. I have observed this behavior on both Sun Solaris 9 and Windows XP Pro (but here I am using unsupported Cygwin w/

Is there a way to detect if the opening of a connection to a pipe was successful or not? Here are two examples # Works > con <- pipe("ls") > res <- open(con, open="r") > print(res) NULL # Does not work > con <- pipe("unknown_command") > res <- open(con, open="r") > 'unknown_command' is not recognized as an

Hi, I'm running R v1.9.0 on WinXP Pro. I noticed that R.exe and Rterm.exe behave differently on Ctrl-C. Starting a Windows Command prompt (cmd.exe) you get from running Rterm.exe: C:\Program Files\R>rw1090\bin\Rterm.exe --vanilla --quiet > ^C > ^C > 1+1 [1] 2 > Sys.sleep(100) # Ctrl-C after a few seconds > ^C > ^C > 1+1 [1] 2 > q() C:\Program Files\R>

Hello, I wonder if it is unwise to name a bundle the same as one of its packages. For instance, I now have a huge package called 'aroma' that I basically want to split up in several smaller packages, say 'aroma.core', 'aroma.io', 'aroma.explore', 'aroma.trial', 'aroma.deprecated' etc, which simplifies maintenance but also the overview. For

Hi, Gordon Smyth brought the following problem to my attention. PROBLEM/"BUG": Using R v1.9.0 alpha for Windows and the latest Rtools from Brian Ripley you get the following problem trying to R CMD build a package (or a bundle); >R CMD build R.basic * checking for file 'R.basic/DESCRIPTION' ... OK * preparing 'R.basic': * checking whether 'INDEX' is

Hi, just in the process of updating my packages for R v2.0.0 and I have not had time to followed the R v2.0.0 discussions so maybe my questions have already been answered. A concern I have is that when creating packages they should be backward compatible with R v1.9.x for a while until all users and computers has migrated to R v2.0.x. It is pretty straightforward to setup my packages so that

What about adding the argument 'flush=FALSE' to read.table() for the option to ignore trailing elements on each row? This feature already exists in scan(), which is called internally by read.table(): flush: logical: if `TRUE', `scan' will flush to the end of the line after reading the last of the fields requested. This allows putting comments after the last

With tryCatch() it is possible to catch interrupts with tryCatch(). Then you can use a 'finally' statement to clean up, release resources etc. However, how can I "protect" against additional interrupts? This is a concern when the hold down Ctrl+C and generates a sequence of interrupts. Example: tryCatch({ cat("Press Ctrl+C...\n"); Sys.sleep(5); }, interrupt =

Before reinventing the wheel, is there a package for working on (nice) sets and intervals, where one can for instance check if a set of intervals contains a scalar, taking the union and intersection of some intervals etc? Example: # Defining the set i = [1,2) + [3.5, 10] i <- c(1,2, 3.5, 10) attr(i, "include") <- c(TRUE, FALSE, TRUE, TRUE) x <- 0:12 # Get

Dear R developers, I will ask a very straightforward question concerning UseMethod's future, because people depending on my code wonder what will happen to it next. In R v2.0.1 NEWS it says o The undocumented use of UseMethod() with no argument is now formally deprecated. and in the R v2.0.1 help(UseMethod) it says 'UseMethod' accepts a call with no arguments and tries to

Hi, I am not sure if this is a bug or a non-implement feature of text-drawing functions with TeX-style expression, but hat() and some of its equals does not get the right "bounding boxes" if they are put in sub- or superscripts. For instance, for the expression 'b[hat(a)]' the hat() seems to shift 'hat(a)' too much to the right of 'b'. Try the below example and

When using write.table() to write data frames the integer columns are padded with unnecessary spaces (0x20) so that these columns are right align if you look at them in a text editor. However, I think it is quite a vast of file size. For instance, I am reading a tab-delimited 4200kb microarray data file and writing it back verbatim using write.table() and it becomes 5100kb, a 20% increase. Is this

Hi, is there a way to check the value of argument 'save' in quit() from within .Last() in my package. I would like to be able to save() an environment if quit("yes") was called and otherwise not. Thanks Henrik Bengtsson Dept. of Mathematical Statistics @ Centre for Mathematical Sciences Lund Institute of Technology/Lund University, Sweden (+2h UTC) +46 46 2229611 (off), +46

Hi, is there are reason for not supporting NULL or "NULL" values for argument colClasses in read.table(), much like you can use NULL values for argument 'what' in scan()? This would help quite a bit when reading large data files where only a few columns are of interest. I've modfied read.table() to so it calls scan(what=...) also with NULLs for the fields to be skipped.

Full_Name: Henrik Bengtsson Version: 1.6.0, 1.5.1 OS: WinXP Pro Submission from: (NULL) (128.250.252.82) The following example, which I tested on both R v1.5.1 and R v1.6.0 on WinXP Pro, shows the problem I encountered when trying to use the class attribute of an environment: # Define method print() for class Environment C print(e) # gives: # [1] "An Environment!" # Exit [R]

First of all, I haven't followed the discussion about the new/upcoming name space support in R so I do not know the purposes or requirements for it, neither its design, and I can only guess. I found the (initial?) notes by Luke Tierney on the Developers Page. Are there any other references? Since it seems that the current implementation (R v1.6.2) of name spaces is a "trial" version

Is there a way of calling the method of the root class directly? Here is an example explaing my question. Everything relates to S3/UseMethod classes and methods. I have an object x of class MicroarrayMatrix, which inherits from class Matrix. The "core" object of x is a simple matrix. In other words, I basically have x <- matrix(logratios, ncol=nbrOfSpots, nrow=nbrOfSlides)

>From R v1.6.0 there has been a new test added to the library() code. This test is performed when library() is ran on a "unix" system and it verifies that the "Built" platform (from the DESCRIPTION file) is "compatible" with the current platform. Here is the code extract from the local function testRversion() of library() that I am talking about: if

I am not sure if what I am asking below should be discussed under r-help or r-devel, so please feel free to move over to r-devel. This is a spin off from Gordon Smyth's question about generic functions and Robert Gentleman's reply. I have tried to raise the question before and I am sure this has been discussed by others, but never on the r-help list what I can see. My concern is that