From ehlers at ucalgary.ca  Fri Apr 23 21:15:07 2010
From: ehlers at ucalgary.ca (Peter Ehlers)
Date: Fri, 23 Apr 2010 13:15:07 -0600
Subject: [Rd] Deferred Default Marker
In-Reply-To: <1272036039.5556.17.camel@punchbuggy>
References: <1272036039.5556.17.camel@punchbuggy>
Message-ID: <4BD1F1BB.2050302@ucalgary.ca>

Terry,

I don't see the problem in R 2.11.0 or R 2.10.1 Patched
(session info for R 2.10.1 below) with Windows (Vista).
I do get warnings about kinship having been built under
R 2.11.0 when I use R 2.10.1.

But I notice that your version of kinship looks somewhat
dated. Is that intentional?

   -Peter Ehlers

 > sessionInfo()
R version 2.10.1 Patched (2010-01-05 r50896)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252

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

other attached packages:
[1] kinship_1.1.0-23 lattice_0.18-3   nlme_3.1-96      survival_2.35-8

loaded via a namespace (and not attached):
[1] grid_2.10.1


On 2010-04-23 9:20, Terry Therneau wrote:
> I've finally narrowed down a puzzling problem: here is the short test
> case.
>
> tmt34% R --vanilla
>
> R version 2.10.0 (2009-10-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
>> temp<- matrix(runif(50), ncol=2)
>> t(temp) %*% temp
>           [,1]     [,2]
> [1,] 7.916016 6.049698
> [2,] 6.049698 7.650694
>
>> library(kinship)
> Loading required package: survival
> Loading required package: splines
> Loading required package: nlme
> Loading required package: lattice
>> t(temp) %*% temp
> `__Deferred_Default_Marker__`
>
> -----------------------------------------
>
> Within the library is a definition of %*% for bdsmatrix objects, which
> is perhaps the issue.  But I'm only guessing since I don't have a clear
> idea what the error message means.  Any hints are appreciated.
>
> The new coxme/bsdmatrix packages need only a couple more functions to be
> a complete replacement for kinship, at which point we will depreciate
> it. (Pedigrees and plotting were finished last weekend!)  But I can't
> quite do that yet. The error does not arise with these newer libraries.
> There have been no changes to kinship for some time.
>
>    Terry Therneau
>
>
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       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
> other attached packages:
> [1] kinship_1.1.0-11 lattice_0.17-26  nlme_3.1-96      survival_2.35-9
>
> loaded via a namespace (and not attached):
> [1] grid_2.10.0
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Peter Ehlers
University of Calgary



[Rd] Deferred Default Marker
Peter Ehlers