[BioC] DNAString ("GC") -- error in nchar?

[Henrik Bengtsson]

I see.  An aroma.affymetrix user on Mac OSX reported a problem with a
package and even after the update the problem remained.  The session
info reported that the package was up to date, but somehow the code of
the problematic function was still from the previous version.  It
turned out that the person did not restart R so the old version was
loaded but sessionInfo() reported the version that was on file, which
was the new version.  For details, see http://tinyurl.com/29wr5m.  In
this Biostrings problem, R has obviously been restarted, but maybe
there was a problem with the installation that causes (part of?) the
old version to be around, while the DESCRIPTION file is updated.
Maybe there are other Biostrings functions you can investigate to tell
if this is the case or not.

/Henrik

On 9/28/07, Herve Pages <hpages at fhcrc.org> wrote:
> Hi Martin, Henrik,
>
> Thanks for looking at this. Maybe you'd like to know that Biostrings defines
> methods for "nchar", hence this line of output at installation time:
>
>   Creating a new generic function for "nchar" in "Biostrings"
>
> See here
>
>   http://bioconductor.org/checkResults/2.1/bioc-LATEST/Biostrings/lamb1-buildsrc.html
>
> for the complete output on lamb1.
>
> There are actually "nchar" methods for BString, BStringViews and BStringAlign objects
> in Biostrings. Could this be related to the problem?
>
> Thanks again!
> H.
>
>
> Henrik Bengtsson wrote:
> > There is almost always a simple explaination.  So, what does
> >
> >> print(nchar)
> >
> > give your in a clean and "non-clean" R session, and especially what
> > environment(s) are reported?
> >
> > Also, scan for all occurances of nchar():
> >
> > res <- apropos("nchar", where=TRUE);
> > names(res) <- search()[as.integer(names(res))];
> > print(res);
> >
> > Any clues?
> >
> > /Henrik
> >
> > On 9/28/07, Paul Shannon <pshannon at systemsbiology.org> wrote:
> >> Good idea, Martin:  in a clean R, nchar works fine.
> >>
> >> Stranger and stranger...
> >>
> >>   - Paul
> >>
> >>
> >> On Sep 28, 2007, at 3:19 PM, Martin Morgan wrote:
> >>
> >>> I wonder what traceback() says immediately after the error, and
> >>> whether you get the message in a clean R (R --vanilla from the command
> >>> line; do not load Biostrings)?
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> >
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