

Hi Terry,

Not aware about the issue, e.g., from

$ uname -a
Linux c06.mrc-epid.private.cam.ac.uk 2.6.9-89.0.23.ELsmp #1 SMP Fri Mar 5 23:27:13 EST 2010 x86_64 x86_64 x86_64 GNU/Linux

I got

> library(kinship)
Loading required package: survival
Loading required package: splines
Loading required package: nlme
Loading required package: lattice
[1] "kinship is loaded"
> temp <- matrix(runif(50), ncol=2)
> temp <- matrix(runif(50), ncol=2)
> t(temp) %*% temp
         [,1]     [,2]
[1,] 8.327462 6.531409
[2,] 6.531409 9.129242
> t(temp) %*% temp
         [,1]     [,2]
[1,] 8.327462 6.531409
[2,] 6.531409 9.129242
> version
               _
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          11.0
year           2010
month          04
day            22
svn rev        51801
language       R
version.string R version 2.11.0 (2010-04-22)

or 

 $ /genetics/data/software/R-2.11.0/bin/R --vanilla

R version 2.11.0 (2010-04-22)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> temp <- matrix(runif(50), ncol=2)
> t(temp) %*% temp
         [,1]     [,2]
[1,] 9.379705 7.471682
[2,] 7.471682 9.046881
> library(kinship)
Loading required package: survival
Loading required package: splines
Loading required package: nlme
Loading required package: lattice
[1] "kinship is loaded"
> t(temp) %*% temp
         [,1]     [,2]
[1,] 9.379705 7.471682
[2,] 7.471682 9.046881


I look forward to the availability of a complete replacement of bdsmatrix/coxme/pedigree packages. There have been simple yet sticky issues such as allowing for unknown status in the affection status which would benefit from an overhaul implementation than revising the present one.

Jing Hua


> From: therneau@mayo.edu
> To: r-devel@r-project.org
> Date: Fri, 23 Apr 2010 10:20:39 -0500
> Subject: [Rd] Deferred Default Marker
> 
> 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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
 		 	   		  
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