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:
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:
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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Program in Computational Biology
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