From murdoch.duncan at gmail.com  Fri Jul  9 17:22:48 2010
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Fri, 09 Jul 2010 11:22:48 -0400
Subject: [Rd] Mysterious behavior
In-Reply-To: <5DBE21404FF5E54C826BE1040C2CD031C919E1@msgebe52.mfad.mfroot.org>
References: <mailman.23.1278669608.14475.r-devel@r-project.org>
	<5DBE21404FF5E54C826BE1040C2CD031C919E1@msgebe52.mfad.mfroot.org>
Message-ID: <4C373EC8.9070206@gmail.com>

On 09/07/2010 10:55 AM, Therneau, Terry M., Ph.D. wrote:
> I had trouble with some tests for the survival suite last night that I
> cannot explain. 
>
> Framework: Ubuntu Linux, R2.11.  
>    For testing survival I have a separate directory and Makefile.  I
> pull everything into the local .RData, no packages, library, or
> namespace.  (It's easier to add test modifications to a routine in a
> chain of calls).  
>    
>    A test of survreg + psline would fail because splines is not
> automatically loaded in this scenario.  In my console window type
> 	> library(splines)
>       > fit <- survreg(Surv(time, status) ~ ph.ecog + spline(age),
> data=lung)
> as the first 2 lines a a new session (the lung data is also saved)
> and up would pop an error message about having <2.10 version of
> survival.  And it is true that I had such a thing in my ~/RLib.  But
> there is no mention of either the local or the system survival library
> when I type search(), and .Autoloaded is NULL. 
>   
Could you show us the result of .libPaths(), search(), searchpaths() and 
sessionInfo()? 

Duncan Murdoch

>   I'm mystified as to how R decided to use that library, and what it was
> trying to pull from it.  I removed it from ~/Rlib and the message went
> away, but now I'm not so sure that this was a good idea.  Is something
> now being automatically snatched out of the standard survival library?
> If so that compromises the integrity of my testbed.  How do I find out?
>
> Terry Therneau
>
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>



[Rd] Mysterious behavior
Duncan Murdoch