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Confusing inheritance problem

5 messages · Uwe Ligges, Terry Therneau, Hervé Pagès

Original
Terry Therneau
# 
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
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
Uwe Ligges
#
On 15.07.2011 23:23, Terry Therneau wrote:
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
1 day later
Terry Therneau
# 
I've packaged the test library up as a tar file at
	ftp.mayo.edu
	directory therneau, file ktest.tar
	login username: mayoftp
             password:  KPlLiFoz
This will disappear in 3 days (Mayo is very fussy about outside access).

In response to Uwe's comments
  1. "2.13.0" is not recent
    It's not the latest, but it is recent.  This is for machines at work where 
where upgrades happen more infrequently
  2. "Matrix not loaded"  
The sessionInfo was only to show what version we have.  Forgetting to load Matrix 
isn't the problem -- when I do that the error is quick and obvious.

 Thanks in advance for any pointers.

Terry T.
On Sat, 2011-07-16 at 19:27 +0200, Uwe Ligges wrote:
1 day later
Hervé Pagès
# 
Hi Terry,

You use a NAMESPACE but you don't import Matrix.
So it looks like the "rowSums" method for CsparseMatrix objects
cannot be found (not sure why because you do have Matrix in the
Depends field so the rowSums generic and methods should be in the
search path).

Anyway, just adding

import(Matrix)

to the NAMESPACE file solves the problem for me.

Cheers,
H.
On 11-07-18 09:16 AM, Terry Therneau wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Terry Therneau
    

    

      
      #
    

  


  

      
Yup, that fixes the problem.  This was also pointed out by Uwe in a personal
email.
  One confusing aspect is that there are two test files in the skeleton package, one of 
which calls rowSums( a dsCMatrix object) at top level, and the other of which does the
same thing within a dispached method.  Only the second one fails.  An interesting puzzle, but not one I'll pursue with any vigor now that we have a fix.

Terry T.

-----Original Message-----
From: Herv? Pag?s [mailto:hpages at fhcrc.org] 
Sent: Tuesday, July 19, 2011 2:54 PM
To: Therneau, Terry M., Ph.D.
Cc: r-devel at r-project.org
Subject: Re: [Rd] Confusing inheritance problem

Hi Terry,

You use a NAMESPACE but you don't import Matrix.
So it looks like the "rowSums" method for CsparseMatrix objects
cannot be found (not sure why because you do have Matrix in the
Depends field so the rowSums generic and methods should be in the
search path).

Anyway, just adding

import(Matrix)

to the NAMESPACE file solves the problem for me.

Cheers,
H.

        
On 11-07-18 09:16 AM, Terry Therneau wrote: