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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