Re: [Rd] Confusing inheritance problem

2011-07-16 Thread Uwe Ligges 



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(kmat0)
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-8LC_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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[Rd] NAMESPACE

2011-07-16 Thread Gabor Grothendieck 
 Packages without explicit ‘NAMESPACE’ files will have a default one created 
 at build or INSTALL time,
 so all packages will have namespaces. A consequence of this is that 
 ‘.First.lib’ functions need to be
 renamed, usually as ‘.onLoad’ but sometimes as ‘.onAttach’.

Couldn't R simply regard .First.lib as the appropriate function to
save many packages from
being needlessly changed?

-- 
Statistics  Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

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