R devel - Jul 2011 - Confusing inheritance problem

I have library in development with a function that works when called
from the top level, but fails under R CMD check.  The paricular line of
failure is
	rsum <- rowSums(kmat>0)
where kmat is a dsCMatrix object.

  I'm currently stumped and looking for some ideas.

  I've created a stripped down library "ktest" that has only 3
functions: pedigree.R to create a pedigree or pedigreeList object, 
	   kinship.R with "kinship" methods for the two objects 
	   one small compute function called by the others
along with the minimal amount of other information such that a call to
   R --vanilla CMD check ktest
gives no errors until the fatal one.

 There are two test cases.  A 3 line one that creates a dsCMatrix and
call rowSums at the top level works fine, but the same call inside the
kmat.pedigreeList function gives an error
        'x' must be an array of at least two dimensions
Adding a print statement above the rowSums call shows that the argument
is a 14 by 14 dsCMatrix.

 I'm happy to send the library to anyone else to try and duplicate.
    Terry Therneau

tmt% R --vanilla
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-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=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] stats     graphics  grDevices utils     datasets  methods
base

On 15.07.2011 23:23, Terry Therneau wrote:
>   I have library in development with a function that works when called
> from the top level, but fails under R CMD check.  The paricular line of
> failure is
> 	rsum<- rowSums(kmat>0)
> where kmat is a dsCMatrix object.
>
>    I'm currently stumped and looking for some ideas.
>
>    I've created a stripped down library "ktest" that has only
3
> functions: pedigree.R to create a pedigree or pedigreeList object,
> 	   kinship.R with "kinship" methods for the two objects
> 	   one small compute function called by the others
> along with the minimal amount of other information such that a call to
>     R --vanilla CMD check ktest
> gives no errors until the fatal one.
>
>   There are two test cases.  A 3 line one that creates a dsCMatrix and
> call rowSums at the top level works fine, but the same call inside the
> kmat.pedigreeList function gives an error
>          'x' must be an array of at least two dimensions
> Adding a print statement above the rowSums call shows that the argument
> is a 14 by 14 dsCMatrix.
>
>   I'm happy to send the library to anyone else to try and duplicate.
>      Terry Therneau
>
> tmt% R --vanilla
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-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=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] stats     graphics  grDevices utils     datasets  methods
> base


Terry,

1. Your R is not recent.
2. You do this without having Matrix loaded (according to 
sessionInfo())? This may already be the cause of your problems.
3. You may want to make your package available on some website. I am 
sure there are people who will take a look (including me, but not today).

Best wishes,
Uwe








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