similar to: Why can't I "unclass" an array?

This arose in testing [.terms and has me confused. data(esoph)?? # use a standard data set t0x <- terms(model.frame( ~ tobgp, data=esoph)) t1 <-? terms(model.frame(ncases ~ agegp + tobgp, data=esoph)) t1x <- (delete.response(t1))[-1] > all.equal(t0x, t1x) [1] TRUE # the above is wrong, because they actually are not the same > all.equal(attr(t0x, 'dataClasses'),

I'm puzzled by as.matrix. It appears to work differently for Surv objects. Here is a session from my computer: tmt% R --vanilla > library(survival) Loading required package: splines > ytest <- Surv(1:3, c(1,0,1)) > is.matrix(ytest) >[1] TRUE > attr(ytest, 'type') [1] "right" > attr(as.matrix(ytest), 'type') [1] "right" >

The survexp function can fail when called from another function. The "why" of this has me baffled, however. Here is a simple test case, using a very stripped down version of survexp: survexp.test <- function(formula, data, weights, subset, na.action, rmap, times, cohort=TRUE, conditional=FALSE, ratetable=survexp.us, scale=1, npoints, se.fit,

I have a local library with functions that interrogates an institution-specific web API, so is not of interest to anyone outside of Mayo. For some reason the R CMD INSTALL command fails. See below: Build the library, then install it. tmt-local2127% R CMD build dart * checking for file ?dart/DESCRIPTION? ... OK * preparing ?dart?: * checking DESCRIPTION meta-information ... OK * installing

I am getting failure of build and check, for an Rd file that has a long argument list. Guess diagnosis: a quoted string beyond a certain point in the argument list is fatal. Example: Use the function below, create an Rd file for it with prompt(). Move the .Rd file to the man directory (no need to edit it) and try building dart.control <- function(server=c("production",

I haven't done any R memory debugging lately, but https://www.mail-archive.com/rcpp-devel at lists.r-forge.r-project.org/msg10289.html shows how I used to have gdb break where valgrind finds a problem so you could examine the details. Also, running your code after running gctorture(TRUE) can help track down memory problems. -Bill On Wed, Feb 7, 2024 at 12:03?PM Therneau, Terry M., Ph.D.

?I've hit a roadblock debugging a new update to the survival package.?? I do debugging in a developement envinment, i.e. I don't create and load a package but rather? source all the .R files and dyn.load an .so file, which makes things a bit easier. ? Running with R -d "valgrind --tool=memcheck --leak-check=full" one of my test files crashes in simple R code a dozen lines

I've finally narrowed down a puzzling problem: here is the short test case. tmt34% R --vanilla R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 > temp <- matrix(runif(50), ncol=2) > t(temp) %*% temp [,1] [,2] [1,] 7.916016 6.049698 [2,] 6.049698 7.650694 > library(kinship) Loading required package:

I've narrowed my scope problems with predict.coxph further. Here is a condensed example: fcall3 <- as.formula("time ~ age") dfun3 <- function(dcall) { fit <- lm(dcall, data=lung, model=FALSE) model.frame(fit) } dfun3(fcall3) The final call fails: it can't find 'dcall'. The relevant code in model.frame.lm is: env <- environment(formula$terms)

My on-screen plots with the latest build are acting strange. If the y label is longer than some small value it is not shown. Here is the script of a job. A pdf graph is fine. I use xubuntu as the windowing system. tmt-local1334% R --vanilla R Under development (unstable) (2017-08-31 r73172) -- "Unsuffered Consequences" Copyright (C) 2017 The R Foundation for Statistical Computing

>>>>> Duncan Murdoch >>>>> on Fri, 5 Apr 2019 11:12:48 -0400 writes: > On 05/04/2019 10:46 a.m., Therneau, Terry M., Ph.D. wrote: >> >> >> On 4/5/19 9:39 AM, Duncan Murdoch wrote: >>> On 05/04/2019 10:19 a.m., Therneau, Terry M., Ph.D. wrote: >>>> Duncan, >>>> ?? I should have

I am trying to clear up all the "NOTE"s before a CRAN submission, but am a bit confused about this one.?? What is it complaining about -- that it doesn't like my name? ... * checking for file ?deming/DESCRIPTION? ... OK * this is package ?deming? version ?1.4-1? * checking CRAN incoming feasibility ... [7s/18s] NOTE Maintainer: ?Terry Therneau <therneau.terry at mayo.edu>?

I've created some Splus code for a microarray problem that - needed to be in C, to take advantage of some sparse matrix properties - uses a cholesky decompostion as part of the computation For the cholesky, I used the cholesky2 routine, which is a part of the survival library. It does just what I want and I'm familiar with it (after all, I wrote it). In Splus, this all works

I have library in development with a function that works when called from the top level, but fails under R CMD check. The paricular line of failure is rsum <- rowSums(kmat>0) where kmat is a dsCMatrix object. I'm currently stumped and looking for some ideas. I've created a stripped down library "ktest" that has only 3 functions: pedigree.R to create a pedigree or

When I run R CMD check on the survival package I invariably get a note: ... * checking for file ?survival/DESCRIPTION? ... OK * this is package ?survival? version ?3.2-6? * checking CRAN incoming feasibility ... NOTE Maintainer: ?Terry M Therneau <therneau.terry at mayo.edu>? ... This is sufficient for the auto-check process to return the following failure message: Dear maintainer,

Where can I find out (and replicate) what options as-cran turns on? The issue: the following lines generate an error in R CMD check --as-cran? for coxme.? But there is no error without as-cran nor is there one when I run the code in a terminal window. ismat <- function(x)? inherits(x, "matrix") || inherits(x, "bdsmatrix") || inherits(x, "Matrix") if

Question: I am trying to impliment a function in R that we use quite regularly in Splus, and it fails due to a lack of the "terms.inner" function in R. The substitute is? Part question and part soapbox: Why remove terms.inner from R? It's little used, but rather innocuous. Mostly soapbox: I figured it was no big deal, as I originally discovered the use of terms.inner from

The model.frame function has trouble with a certain type of really long formula. Here is a test: tname <- paste('var', 1:50, sep='') tmat <- matrix(rnorm(500), ncol=50, dimnames=list(NULL, tname)) tdata <- data.frame(tmat) temp1 <- paste( paste(tname, tname, sep='='), collapse=', ') temp2 <- paste("~1 + cbind(", temp1, ")")

I'd like to get interaction terms in a model to be in another form. Namely, suppose I had variables age and group, the latter a factor with levels A, B, C, with age * group in the model. What I would like are the variables "age:group=A", "age:group=B" and "age:group=C" (and group itself of course). The coefficients of the model will then be the age effect

This run was done this AM on my linux box, and older 32 bit Dell optiplex (core 2 duo). The failure message is at the very end. (It's due to be replaced in a couple of weeks.) The sequence of steps was svn up tools/rsync-recommended ./configure make make check-all |& tee zzz Terry T. Result of ./config R is now configured for i686-pc-linux-gnu Source directory: .