similar to: setGeneric and file order in a package

Full_Name: Ross Boylan Version: 2.10.0 OS: Windows XP Submission from: (NULL) (198.144.201.14) Some of the help for setGeneric seems to have been garbled. In the section "Basic Use", 5th paragraph (where the example counts as a single line 3rd paragraph) it says <quote> Note that calling 'setGeneric()' in this form is not strictly necessary before calling

Is it safe to call setGeneric twice, assuming some setMethod's for the target function occur in between? By "safe" I mean that all the setMethod's remain in effect, and the 2nd call is, effectively, a no-op. ?setGeneric says nothing explicit about this behavior that I can see. It does say that if there is an existing implicity generic function it will be (re?)used. I also tried

I've attached a script I wrote that pulls all the setGeneric definitions out of a set of R files and puts them in a separate file, default allGenerics.R. I thought it might help others who find themselves in a similar situation. The "situation" was that I had to change the order in which files in my package were parsed; the scheme in which the generic definition is in the

Is there any good source of information on how S4 classes (and methods) work from C? E.g., for reading how to read a slot value how to invoke a method how to test if you have an s4 object For writing, how to make a new instance of an S4 object. I've found scattered hints in the archive, including a link to a talk on this subject "I am using C code to create an S4 object based on

Originally I made a function yearStop that took an argument "object". I made a generic, but later changed the argument to "x". R keeps resurrecting the old definition. Could anyone explain what is going on, or how to fix it? Note particularly the end of the transcript below: I remove the generic, verify that the symbol is undefined, make a new function, and then make a

I have a small S4 class for which I've written a page grouping many of the accessors and replacement functions together. I would be interested in people comments on the approach I've taken. The code has a couple of decisions for which I could imagine alternatives. First, even simple get/set operations on class elements are wrapped in functions. I suppose I could just use myinstance at

This is a correction to my previous message, I forgot to swap two lines in the body of setMakeGenericMethod. Sorry about that. The correct (full message) reads like this: Hi, This works > setGeneric("clear", function(obj) standardGeneric("clear")) [1] "clear" but this doesn't. Why? > funName <- "clear" > setGeneric(funName,

I have classes A and B, where B contains A. In the implementation of the group generic for B I would like to use the corresponding group generic for A. Is there a way to do that? I would also appreciate any comments if what I'm trying to do seems like the wrong approach. Here's a stripped down example: setClass("A",

well, the next place to go, if fsck isn't enough would be to to try debugfs(1) man debugfs. On Wed, Nov 18, 2015 at 8:39 PM, Boylan, Ross <Ross.Boylan@ucsf.edu> wrote: > I guess some of the trouble was that the virtual disk was mounted > read-only at the VM level. When I mounted read/write I was able to do > fsck, which gave messages about replaying the logs and a couple

Dear fellow R users, I am now investing time in learning how to use compiled C code to produces functions that can be used in R. I am just starting, and there is much that I need to learn, so I have a question that might be straight forward. I am learning how to use function in the C library GSL (gnu scientific library), to write C code, that I then plant to use in R. Is there any problem in

Ivan, thank you for the tips; they allowed me to move on to the next problems. By building the tar file first and checking it later, and fixing several other problems I got R CMD check to work. It does *not* delete inst/doc. It also does not run boostrap.R, as far as I can tell, presumably because only devtools does. Check within RStudio continues to delete inst/doc, so this behavior is

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 creates has no methods in it. >

In the last few days I've received couple of messages pointing out that our SparseM package fails to install on the patched version of 1.7.0. Laurent Gaultier kindly suggested that replacing: setGeneric("as.matrix.csr") by setGeneric("as.matrix.csr", function(x, nrow, ncol, eps) standardGeneric("as.matrix.csr")) was sufficient to fix the problem.

Hi the list When two setGeneric occurs on the same function, the second erage the first and erase all the function previously define. Is it possible to prevent that ? Is it possible to declare a setGeneric that can not be erased later ? Something like the |sealed for setMethod...| || |Thanks| || Christophe

I seem to have run into https://bugzilla.redhat.com/show_bug.cgi?id=855640, because when I tried the fix/work-around at the end (comment 11), ethtool -K eth0 gro off, my download speed by speedtest went from undetectable to ~150Mb/s. However, it was not able to connect for the upload test, and so something may still be off. Non-virtual machines can do the upload test, so it's not just a

Hi list, Calling setGeneric()/setMethod() from within the .onLoad() hook of MyPkg package produces the following error: > gctorture(TRUE) > library(MyPkg) .onLoad(): ok1 .onLoad(): ok2 Error : protect(): protection stack overflow Error : .onLoad failed in 'loadNamespace' for 'MyPkg' Error: package/namespace load failed for 'MyPkg' This is with

Apparently Scheme is clever and can turn certain apparently recursive function calls into into non-recursive evaluations. Does R do anything like that? I could find no reference to it in the language manual. What I'm wondering is whether there are desirable ways to express recursion in R. Thanks. -- Ross Boylan wk: (415) 514-8146 185 Berry St #5700

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

I tried the following (relevant excerpt only) setMethod("likelihood", signature(spec="Specification", covs="vector", states="vector"), function(spec, covs, states) { #### setMethod("likelihood", signature(model="Model", path="matrix"), function(model, path) { This

I have a package that can use rmpi, but works fine without it. None of the automatic test code invokes rmpi functionality. (One test file illustrates how to use it, but has quit() as its first command.) What's the best way to handle this? In particular, what is the appropriate form for upload to CRAN? When I omitted rmpi from the DESCRITPION file R CMD check gave <quote> * checking