similar to: Problem with dyn.load in R 2.13.0

Martin, I am aware of --vanilla; I use it myself for some testing. In this case R_LIBS_USER was set externally (part of my login) and does not involve any of the R scripts. That means it is inherited by any subprocess. For example: tmt1495% R --vanilla --no-environ R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing

I have a local library which depends on the expm library. The expm library is loaded into my personal space and I have the environment variable R_LIBS_USER set appropriately. The command "library(expm)" works just fine from the command line, and in fact the package works if I do the source() and dyn.load() commands by hand. The following sequence works: tmt% R CMD build

R version 2.9.0 running on Centos (Red Hat linux). I have a pair of packages coxme and bdsmatrix. The latter is installed in my local library (I don't have permission for global install at work.) That is, it is in the location pointed to in R_LIBS_USER. In R, the command library(bdsmatrix) works fine. Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C routines, which

Dear all, As the object of this mail suggests, the methods package is not loaded by default in R2.13 when using Rscript whereas it is loaded when using an interactive session. An example with the metafor package : library(metafor) example(addpoly.rma) this works in an interaction R shell, but put it in a .R file and use it with Rscript, it won't work until you added library(methods)

Martyn, No, that didn't work. One other thing in the mix (which I don't think is the issue) is that I call one of the C-entry points of expm. So the DESCRIPTION file imports expm, the NAMESPACE file imports expm, and the init.c file is #include "R.h" #include "R_ext/Rdynload.h" /* Interface to expm package. */ typedef enum {Ward_2, Ward_1, Ward_buggy_octave}

Dear all, I have encountered the following problem where coxme seems to allow model with only random effect in R 2.11.1 but not in R 2.13.0. Following is the error message using rat example data. Any comment on this is appreciated. In R2.13 > library(coxme) > rat1 <- coxme(Surv(time, status) ~ rx + (1|litter), rats) > rat0 <- coxme(Surv(time, status) ~ (1|litter), rats)

If x has an S3 class then sort.int(x) returns a value without an S3 class but which has the is.object flag set, which, I think, causes identical() give a false/misleading report: > x <- structure(1:3, class="unrecognizedClass") > y <- sort.int(x) > t <- 1:3 > identical(y, t) # expect TRUE [1] FALSE > identical(as.vector(y), as.vector(t)) # expect

Dear R users, I have a desktop computer and a laptop, both of them with Ubuntu Lucid. The former has R2.10 installed from Ubuntu repositories (this is the most recent version in the repositories), while the latter has R2.13 from the CRAN repositories. I noticed that postscript files generated with R2.10 are "better" than files generated with the latest release of R, in particular for

Hi, I would appreciate some help with a very basic problem in using pgfSweave. That is, dealing with the sweave.sty file. After some googling, I did the following : (1) copied the sweave.sty file to my trial folder and (2) added the line?? \usepackage{Sweave}?? to the Rnw file. Are there more elegant ways of dealing with this issue? I have read something about letting Miktex know about the

Hello, The following piece of code works fine in R.2.10 (ubuntu): switch(distr,         normal    = {if (is.infinite(param["desv"]))                      n <- c(n,"La desv. estándar no puede ser Inf.")                    if (param["desv"]<0)                      n <- c(n,"La desv. estándar no puede ser <0.")                    },        

I am trying to upgrade to R 2.14 from R 2.13.1 I have compied all the libraries from the 'library' directory in my existing installation (2.13.1) to the installed R 2.14. Now I want to uninstall the old installation (R 2.13.1) and I get the error: Internal Error: Cannot find utCompiledCode record for this version of the uninstaller. Any ideas? Kevin [[alternative HTML

Hola a todos. Un problema dos pasos. Quiero desde RStudio trabajar con dos versiones de R (pongamos R2.13 y R2.15) desde Linux, Ubuntu 10.04 (lucid). Ya tengo instalada la R.2.15.1. Por defecto trabajo con ella. Pasos que creo he de dar: 1º. Instalar dos versiones de R en la misma maquina. ¿Como se hace?. Me estoy metiendo con el PATH y tal... hay algún protocolo clarito por ahí? 2º.

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)

Dear Helpers: If you know how to fit a Weibull model using R, you are my savior for my project. The hazard ramda is specified as t^alpha * (1+a*dose*exp(-b*dose)). Or, can we modify the Cox model to capture the proportional part above? Here t is the survial time, dose is a subject received in a exposed group. Thank you a lot. Boshao

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

Hi, I am trying to install a bunch of packages via command line and can use some help in getting it right. My env is a freshly setup OpenSuse 11.4 on an amd desktop. I have not yet installed gcc (Will I need gcc to install packages? I have installed make, assuming R might need it.). I have tried it both under R2.12 and R2.13. I have a list of packages to install such as fImport, fGarch, zoo,

Dear All: I have a question on using coxph for multiple genes: I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data. However, I don't know how to work with the result for each gene: survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg.

I can't seem to get a histogram of dates: tmt910% R --vanilla R version 2.13.0 (2011-04-13) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 ... > temp <- as.Date(1:200, origin="1970/01/01") > range(temp) [1] "1970-01-02" "1970-07-20" > hist(temp) Error in .Internal(inherits(x, what, which)) : 'x' is missing

On Thu, 2017-02-09 at 09:52 -0600, Therneau, Terry M., Ph.D. wrote: > Martin, > ? I am aware of --vanilla; I use it myself for some testing.??In this case R_LIBS_USER was? > set externally (part of my login) and does not involve any of the R scripts.??That means? > it is inherited by any subprocess.??For example: > > tmt1495% R --vanilla --no-environ > > R version 3.3.1

Hi Allen and list, See the code below.? I've tried it on R2.13 and R2.8.0 using either heatmap.plus 1.3 or the latest.? All gave the same results.? The problem is in the last line: when I tried to plot two different color bars, the one corresponding to "cm.colors(10)" is not correct (it starts with one black and one red.? Not sure where they're from?) Any ideas? Thanks!