From therneau at mayo.edu  Thu May  2 21:05:59 2013
From: therneau at mayo.edu (Terry Therneau)
Date: Thu, 02 May 2013 14:05:59 -0500
Subject: [Rd] loading of an unwanted namespace
Message-ID: <5182B917.9050709@mayo.edu>

I have a debugging environment for the survival package, perhaps unique to me, but I find 
it works very well.
To wit, a separate directory with copies of the source code but none of the package 
accuements of DESCRIPTION, NAMESPACE, etc. This separate space does NOT contain a copy of 
src/init.c
Within this I use R --vanilla, attach my .RData file, survival.so file, and away we go.

That is, until my first useage of it today under R 3.0. My runs get into trouble with 
messages about
"conflicts with the survival namespace". My problem is that I can't figure out where or 
how the name space is being searched out and attached. Any hints on where to look would be 
appreciated. This "magical" load is
kind of spooky.

Here is a session that displays it. The "setup.s" file does the dyn.load and attaches some 
data sets.

tmt-local3499% R --vanilla

R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)> source('setup.s')
 > sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: i686-pc-linux-gnu (32-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
 > search()
[1] ".GlobalEnv" "file:../.RData" "file:../data/.RData"
[4] "package:splines" "package:stats" "package:graphics"
[7] "package:grDevices" "package:utils" "package:datasets" > coxph(Surv(time, status) ~ 
age, data=lung)
Call:
coxph(formula = Surv(time, status) ~ age, data = lung)


coef exp(coef) se(coef) z p
age 0.0187 1.02 0.0092 2.03 0.042

Likelihood ratio test=4.24 on 1 df, p=0.0395 n= 228, number of events= 165
 >
 > # That worked fine, but the next fails
 > coxph(Surv(time, status) ~ pspline(age), data=lung)
Error in FUN(X[[2L]], ...) :
(converted from warning) failed to assign RegisteredNativeSymbol for Cagfit5a to Cagfit5a 
since Cagfit5a is already defined in the ?survival? namespace
 >
 > sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: i686-pc-linux-gnu (32-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
 >

[10] "package:methods" "Autoloads" "package:base"
 >
 > options(warn=2)


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[Rd] loading of an unwanted namespace
Terry Therneau