From mtmorgan at fhcrc.org  Thu May  2 22:43:55 2013
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 02 May 2013 13:43:55 -0700
Subject: [Rd] loading of an unwanted namespace
In-Reply-To: <5182CE21.4080901@gmail.com>
References: <5182B917.9050709@mayo.edu> <5182CE21.4080901@gmail.com>
Message-ID: <5182D00B.5020503@fhcrc.org>

On 05/02/2013 01:35 PM, Duncan Murdoch wrote:
> 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.

   trace(loadNamespace, quote(if (package == "survival") recover()))

will break into ?recover when survival is being loaded.

Martin


>
> 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)
>>
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
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>>
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>
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[Rd] loading of an unwanted namespace
Martin Morgan