loading of an unwanted namespace

On 13-05-02 3:05 PM, Terry Therneau wrote:

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.

I don't know a direct way to find this, but you could add some debugging code to
the .Onload function in survival, e.g. to print what the stack is like when it's
loading.  That should be informative.

Duncan Murdoch

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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