similar to: Quantile issue

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

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 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",

Is it a bug that quantile() can return a lower sample quantile for a higher probability? > ##### quantile returns decreasing results with increasing probs (data at the end of the message) > quantile(x2, (0:5)/5) 0% 20% 40% 60% 80% -0.0014141174 -0.0009041968 -0.0009041968 -0.0007315023 -0.0005746115 100% 0.2905596324 >

A user asked me about this and I can't figure it out. tmt% R R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > library(survival) > data(cgd0) Warning message: In data(cgd0) : data set ?cgd0? not found ---- The data set is present and can be

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 all, I am running into a snag using quantile function in stats. Basically, I don't understand why the loop below throws the error that it does. test.data <- rnorm(1000, 0, 1) for (i in seq(0.00001, 0.001, 0.00001)){ test <- quantile(test.data, probs=seq(0,1,i)); print(i); } It runs fine from 1e-05 to 0.00024, but then throws the error Error in quantile.default(test.data,

The submission guide has the following cryptic (to me) sentence: ?? "Reasonable compression should be used for data (not just .rda files) " The survival pacakge has a fairly large number of data files --- exactly what should I be doing??? xz compression? Terry T.

I found an issue with the data() command this evening when working on the survival package. 1. I have a lot of data sets in the package, almost all used in at least one vignette, help file, or test.? As a space saving measure, I have bundled many of them together, i.e., the file data/cancer.rda contains 19 data sets, many of them small. The resulting file (using xz compression) is quite a bit

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" >

This question likely has a 1 line answer, I'm just not seeing it. (2, 3, or 10 lines is fine too.) For a vector I can do group <- match(x, unqiue(x)) to get a vector that labels each element of x. What is an equivalent if x is a data frame? The result does not have to be fast: the data set will have < 100 elements. Since this is inside the survival package, and that package is on

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

First, as others have said please obey the mailing list rules and turn of First, as others have said please obey the mailing list rules and turn off html, not everyone uses an html email client. Here is your code, formatted and with line numbers added. I also fixed one error: "y" should be "status". 1. fit0 <- coxph(Surv(futime, status) ~ x1 + x2 + x3, data = data0) 2. p

Martin, Thanks for taking a quick look. Yes it looks like it must be something local. I've done the following to make sure I have a clean box: reboot sudo apt-get update sudo apt-get upgrade Rerun the "svn up" command and do a make distclean svn up tools/rsync-recommended ./configure make The problem persists in 2017-09-01 r73179 I pulled the source

?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 have an ASAN enabled version of R-devel on my test machine, and can get it to relably crash.? Here is the first part of the session: tmt-local2434% R --vanilla R Under development (unstable) (2019-06-28 r76752) -- "Unsuffered Consequences" Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under

Hi, I am trying to use quantile regression to perform weighted-comparisons of the median across groups. This works most of the time, however I am seeing some odd output in summary(rq()): Call: rq(formula = sand ~ method, tau = 0.5, data = x, weights = area_fraction) Coefficients: Value Std. Error t value Pr(>|t|) (Intercept) 45.44262 3.64706 12.46007

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,

> On Sep 18, 2017, at 5:13 AM, Therneau, Terry M., Ph.D. <therneau at mayo.edu> wrote: > > This question likely has a 1 line answer, I'm just not seeing it. (2, 3, or 10 lines is fine too.) > > For a vector I can do group <- match(x, unqiue(x)) to get a vector that labels each element of x. > What is an equivalent if x is a data frame? > In the past I've