search for: promptclass

promptClass fails to identify methods associated with the class. Here is a fix: Index: promptClass.R =================================================================== --- promptClass.R (revision 41719) +++ promptClass.R (working copy) @@ -165,7 +165,7 @@ if (nmeths > 0) { .meths....

I've had repeated problems with promptClass missing methods, usually telling me a class has no methods when it does. In my current case, I've defined an S4 class "mspathCoefficients" with a print method setMethod("print", signature(x="mspathCoefficients"), function(x, ...) { # etc The file promptClass crea...

Hi! Have written some functions with signature "numeric". eg. setGeneric("foo", function(object,...) standardGeneric("foo")) setMethod("foo",signature(object="numeric"),def = .... To generate the Rd file sceleton i use > promtClass("numeric") A shell of class documentation has been written to the file

...package has been committed to the r-devel branch. There are a lot of changes, mostly non-visible, many of those to tighten up some possible problems. For example, slot assignment now checks the validity of the value being assigned, and basic classes cannot be overriden. There is a version of the promptClass function by Vince Carey, to produce shell of documentation for a class. (There is also a promptMethods function to do the same for methods.) One point to note (it's a difference from Vince's original version) is that promptClass and promptMethods produce alias's specialized for class...

Hi, I have been using R for a while. Recently, I have begun converting my package into S4 classes. I was previously using Rdoc for documentation. Now, I am looking to use the best tool for S4 documentation. It seems that the best choices for me are Roxygen and Sweave (I am fine with tex). Are there any users of Roxygen or Sweave who can comment on the strengths or weaknesses of one or othe

Hi! I have renamed some functions and deleted others. I have noticed that R CMD check complains only about newly added functions, but documented non-anymore-existing functions seem not to matter. I knew about prompt and promptMethods promptClass. They are extremely useful if you are starting to write a package. But what with existing packages that have to be rewritten? Having code and documentation in one place would be a great help. Has anyone a tool which is able to generate from appropriately commented R-code files (e.g. <<exampl...

1. I'm putting together my first package that uses S4 classes and objects. I'd like to document them, but I'm not sure what the documentation should look like, and package.skeleton doesn't produce any at all for the classes or methods. Are there any good examples to follow? 2. How do I do the equivalent of debug(foo), when foo is an anonymous function being used as a method?

...* using the code_files option (since dumpMethod does not exists) * providing the list of the class (since sys.source does not compile setClass) * using the same path than package.skeleton At this three conditions, package.skeleton.S4 will : - modify the DESCRIPTION package, - run promptClass on the classes gived in the list, - run promptMethod on all the methods related to the classes gives in the list. I tryed to solve the sys.source problem, but I am not good enough in R to do it myself. I do not even know if it is something hard to do or very easy. So I post this uncompleted fu...

Dear all, I am trying to write a package using formal methods and classes from the methods package. I have not been able to get the package to pass rcmd check without warnings, because rcmd check does not recognize my generic functions as code objects and therefore queries why they have documentation entries. I have isolated the problem in a very small trivial example which I give below. I

...st foo) 3) the interface provided by a class (for B, foo and bar) 4) the various implementations of a particular method All of these can be discovered dynamically by the user. The problem is that current documentation system attempts to reproduce this dynamic information in static pages. prompt, promptClass and promptMethods functions generate templates that contain much of the information (or at least there supposed to; they seem to miss stuff for me, for example saying there are no methods when there are methods). This is helpful, but has two weaknesses. First, the class developer must enter very...

Hi the list, Using S4, how can we create a package? In "S4 Classes in 15 pages, more or less", they put all the classes definition in a function that will be called at the opening of the library and they add "by hand" a Rd file. Is it the only way ? Is there something like "S4.package.skeleton"? Thanks Christophe

1. promptClass generated a file that included \section{Methods}{ No methods defined with class "mspathDistributedCalculator" in the signature. } Yet there are such methods. Is this a not-working yet feature, or is something funny going on (maybe I have definitions in the library and in the global works...

...and the new code did indeed correctly find slight documentation inconsistencies in quite a few cases (including our own recommended package 'Matrix'), so *is* helpful ..... even though you at first may experience the new warnings as annoying ;-) Feedback is welcome, and patches to improve promptClass() to automatically mark slots from superclasses as only *optional* to document are even more welcome ! Martin Maechler, ETH Zurich

...) but not in xxx.-methods.Rd. As a result long signatures may overfill lines or go off the page. For example, some entries for "[<-" are wrapped on two lines in 'Matrix-class.Rd' below and do not overfill the line, while in the second case they do. > library(Matrix) > promptClass("Matrix") A shell of class documentation has been written to the file 'Matrix-class.Rd'. > promptMethods("[<-",file="proba.Rd") A shell of methods documentation has been written to the file 'proba.Rd'. The syntax is very similar in both cases...

Hi, I'm documenting a package that makes heavy use of S4 methods at the moment, and I'm having a hard time from keeping the PDF output of Rd from looking really terrible. First of all, what is the preferred way to actually document S4 methods? When I use promptClass/promptMethod, I get a style that doesn't use the \S4method macro and puts the entire function signature into a \item. The generated PDFs look terrible because there is no way to get line breaks into these \item titles (?) and so a lot of lines just overflow the page. Manually writing the docs...

...age that uses S4 classes and > > objects. I'd like to document them, but I'm not sure what the > > documentation should look like, and package.skeleton doesn't produce > > any at all for the classes or methods. > >Hmm, sounds as if it should. > >Meanwhile, promptClass and promptMethods generate skeleton >documentation. > > > > > Are there any good examples to follow? > >The bioconductor packages (e.g, Biobase) have some examples. ... >John > > > > > Duncan Murdoch > > > > ___________________________________...

...#Rd files? Would someone be interested in something similar. If #so let me know please. # # #/E # # # #*********** REPLY SEPARATOR *********** # #On 9/17/2004 at 9:07 AM Mark.Bravington@csiro.au wrote: # #>>>Wolski wrote: #>>> #>>>#I knew about prompt and promptMethods promptClass. They are #>>>#extremely useful if you are starting to write a package. But #>>>#what with existing packages that have to be rewritten? #>>># #>>>#Having code and documentation in one place would be a great #>>>#help. Has anyone a tool which is able t...

...but in fact only returned k. It now returns all n eigenvalues. cmdscale(add = TRUE) failed to centre the return configuration and sometimes lost the labels on the points. Its return value was described wrongly (it is always a list and contains component ac). ? promptClass() in package methods now works for reference classes and gives a suitably specialized skeleton of documentation. Also, callSuper() now works via the methods() invocation as well as for initially specified methods. ? download.file() could leave the destination file open if th...

...but in fact only returned k. It now returns all n eigenvalues. cmdscale(add = TRUE) failed to centre the return configuration and sometimes lost the labels on the points. Its return value was described wrongly (it is always a list and contains component ac). ? promptClass() in package methods now works for reference classes and gives a suitably specialized skeleton of documentation. Also, callSuper() now works via the methods() invocation as well as for initially specified methods. ? download.file() could leave the destination file open if th...

...underflow" warning is no longer shown in legacy quartz() device. o formatC() now limits 'digits' to 50 to avoid problems in C-level sprintf in some OSes. o seq.int(x, y, by=z) gave 'x' (and not an error) if 0 > (y-x)/z > -1. o promptClass() now lists methods, including those for generics in other attached packages. o Connection-related functions such as readBin() no longer crash when supplied with a non-connection object. o as.character.srcref() didn't handle bad srcref objects cleanly. o pre...