similar to: R CMD CHECK WARNING inappropriate for S4 method?

The GeneSetCollection class in the Bioconductor package GSEABase extends 'list' > library(GSEABase) > showClass("GeneSetCollection") Slots: Name: .Data Class: list Extends: Class "list", from data part Class "vector", by class "list", distance 2 Class "AssayData", by class "list", distance 2 If I create

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript -e 'load("c2.RData"); c2[1]' ***

Hi, I installed R-3.1.1 on AIX-5.3 and my installation hanged up while installing Matrix Package. so i killed the gmake ; gmake install the software nad tired installing Matrix package manually - [ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]> /gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix the package compiled successfully but while loading Matrix package the

Hi, I've been using the package "graph" in the BioConductor assortment and writing some functions based on its classes. My question is not specific to this package or BioConductor (I think), but it serves as a useful example. I recently wanted to look at the code for the function "edgeMatrix" for the class "graphNEL". Usually I would type > func.foo and

Hello everyone, Im working with graphNEL object and want to extract all the nodes which have adjacent nodes with at least 20 nodes in between them. acc(graph, graphnodes) obviously provides a list for the accessable nodes of every node from a node and a number of the edges between them. Like this: $`hsa:8379` hsa:100131844 hsa:10393 hsa:246184 hsa:29882 hsa:29945 1

Dear ALL I want to load "HTSanalyzeR", It 's necessary to load "igraph" package. This time I see this error: library(igraph) library(HTSanalyzeR) Loading required package: GSEABase Loading required package: Biobase Error: package 'Biobase' is not installed for 'arch=i386' > I 'll be glade if you help me [[alternative HTML version deleted]]

Hello, Most likely I'm doing something wrong, but am at a loss as to what the issue is. I have a clean checkout of trunk here: ?? ~/svn/r-devel/R$ svn info ?? Path: . ?? Working Copy Root Path: /home/btyner/svn/r-devel/R ?? URL: https://svn.r-project.org/R/trunk ?? Relative URL: ^/trunk ?? Repository Root: https://svn.r-project.org/R ?? Repository UUID:

Can you please show code example, how to draw graph with some nodes and edges, but with weights. I only found here http://www.bioconductor.org/packages/release/bioc/vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf- Using edge weights for labels, but... Here an example: > library("graph"); library(Rgraphviz) > myNodes = c("s", "p", "q", "r") >

Hi Can some one please point out where i am wrong. I am trying to position set of nodes column-wise in cytoscape using RCytoscape A----D B----E C----F ------------------- g <- new ('graphNEL', edgemode='undirected') cw <- CytoscapeWindow ('smallExample', graph=RCytoscape::makeSimpleGraph()) layout (cw, 'jgraph-spring') redraw(cw) nodesFr = c('A',

Duncan that does indeed look to be the case. Many thanks! In particular, tests/reg-tests-1d.R optionally loads the Matrix namespace which allows the test to succeed. Compare: ~/R-rc_2019-04-21_r76409/bin/Rscript -e "options(warn=2); library(Matrix); res <- findMethods('isSymmetric'); print('success')" [1] "success" versus

Hi, I want to ask for a small help for creating an instruction that calls e member method of an object. I suppose that this is not a headache but I am impatient in learning :) I would be very thankful if you can show me an example snippet code that does this in LLVM. Below is described my case. Let's say I have a class TestClass class TestClass { int testMethod(int a); } and I want to

Using Rgraphviz, I draw the undirected graph with vertices A,B,C and D and edges A:B, B:C, C:D, D:A, A:C. I want the vertices A and B to be red and C and D to be blue. The problem is the following: I want the edges A:B and B:C to be green and the edges C:D and C:A to be yellow, while the edge A:C can have the default colour black. I assume that I have to specify this using the edgeAttrs-argument

Hi Ferad, On Wed, 2007-04-04 at 19:48 +0200, Ferad Zyulkyarov wrote: > Hi, > > I want to ask for a small help for creating an instruction that calls > e member method of an object. I suppose that this is not a headache > but I am impatient in learning :) I would be very thankful if you can > show me an example snippet code that does this in LLVM. Below is > described my

Hi- I'm running Vista64 Business and trying to use a package called RGraphViz. Unfortunately, when I try to plot a graph using this package it causes RGUI.EXE to crash. This package has no problem working in WinXP 32-bit. Is there any way to get useful information as to why it crashes? Here's my commands: > library(Rgraphviz) Loading required package: graph Loading required

I don't understand the following behavior for a simple S3 class. The auto-printing at the command line doesn't behave as I expect. I'm probably missing something, but it might be a bug. > print.testClass <- function(x, ...) cat("Class:", class(x), ":", x, "\n") > structure(1, class = "testClass") Class: testClass : 1 > print(1 *

Hi, I'm trying to create a package that contains reference class definitions from which users can create reference objects, but there seems to be something awry. My toy example creates an empty package via package.skeleton('TestClass') to which I add the following R code: TestClass <- setRefClass('TestClass',fields=c('name')) Unfortunately my R console output

Hello, I am the maintainer of the stringkernels package and have come across a problem with using S3 objects in my S4 classes. Specifically, I have an S4 class with a slot that takes a text corpus as a list of character vectors. tm (version 0.5) saves corpora as lists with a class attribute of c("VCorpus", "Corpus", "list"). I don't actually need the

Is it possible to override the $new(...) in the reference class generator? I have tried adding a "new" method to the methods of the class, but that is obviously not correct. I have also tried adding it to the class generator, but the class generator still uses the default constructor. As a simple example, this is the current interface: TestClass <- setRefClass

I edit two files named test.h,test.cpp as follow: ///////////////test.h////////////////////////////////////////////////////////////////class TestClass { private: int fTotal; public: TestClass(); ~TestClass(); };///////////test.cpp/////////////////////////////////////////////////////////////////////////////#include "test.h" TestClass::TestClass() { fTotal = 2; }

Hi all, this is my first post in R devel? sorry if I lost some of the guidelines. Anyway this is my problem: Version: R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) I want to make an S4 class that use the output object of the function of nls.lm as a slot: setOldClass("nls.lm") setClass ( Class="TestClass",