R help - Oct 2009 - na.omit leaves cases with NA's intact

Strange, this normally works, but in a recent run, I have a data set in an
xts format, that has a lot of NA's in a few of the variables in the leading
and trailing positions, due to some lagging calculations. Before running an
analysis, I use

newdata<-na.omit(orginaldata)

and normally a

dim(newdata)

shows the fewer rows. Now, for some reason I do this operation and see that
hundreds of rows SHOULD be removed, (I can plainly see the NAs in there) and
even test is.na(orginaldata$variable) and get a clear "TRUE", but the
case
still remains after the "na.omit" operation. Yes, I'm spelling it
right.

I'm doing this with many sets of data, and it works great except for this
one data set....

Any idea if there are limits on when this function works, or more
importantly, if there is a "manual" way to do it as a workaround?

	[[alternative HTML version deleted]]

What class is 'orginaldata' (and its columns if a data frame)?
Note that packge xts defines methods for na.omit:
> library(xts)
...
> methods(na.omit)
[1] na.omit.data.frame* na.omit.default*    na.omit.ts*
[4] na.omit.xts*

so this is possibly something peculiar to package xts.  See the footer 
of this message: a reproducible example would help enormously in 
finding the root cause here.

On Sat, 31 Oct 2009, David L. Van Brunt, Ph.D. wrote:
> Strange, this normally works, but in a recent run, I have a data set in an
> xts format, that has a lot of NA's in a few of the variables in the
leading
> and trailing positions, due to some lagging calculations. Before running an
> analysis, I use
>
> newdata<-na.omit(orginaldata)
>
> and normally a
>
> dim(newdata)
>
> shows the fewer rows. Now, for some reason I do this operation and see that
> hundreds of rows SHOULD be removed, (I can plainly see the NAs in there)
and
> even test is.na(orginaldata$variable) and get a clear "TRUE", but
the case
> still remains after the "na.omit" operation. Yes, I'm
spelling it right.
>
> I'm doing this with many sets of data, and it works great except for
this
> one data set....
>
> Any idea if there are limits on when this function works, or more
> importantly, if there is a "manual" way to do it as a workaround?
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595