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

Henrik Bengtsson hb at stat.berkeley.edu
Fri Sep 28 22:32:24 CEST 2007


Hi,

go to http://www.bioconductor.org/.  Follow the link "For Developers"
and then "2.1 check reports" to get to:

  http://bioconductor.org/checkResults/2.1/bioc-LATEST/

which is list daily checks on all BioC v2.1 (devel) packages, which is
what you use if you run R devel (v2.6.0).  Scroll down to 'Biostrings'
and you'll see that all its builds and tests are reported as "OK".

In other words, it most likely a problem with your setup, and not the
package.  Compare the version numbers of your packages in
sessionInfo() with existing ones.  Since, it looks like yours are up
to date, the next thing I would check is your R version.  On the top
of the BioC check page you'll find that "R v2.6.0 RC (2007-09-26
r42991)" was used.  Your R v2.6.0 is from 2007-09-12.  Since we're
getting close to the release date of R v2.6.0, things tend to get
updated more frequently.  So, update R and retry.

Hope this helps

Henrik

PS. When you see error like "2 arguments passed to .Internal(nchar)
which requires 3" reporting on mismatching # arguments on internal
functions it is very likely that there has been updates in either a
package or in base R. DS.


On 9/28/07, Paul Shannon <pshannon at systemsbiology.org> wrote:
> The Biostrings vignette has some code like this:
>
>  > library(Biostrings)
>  > b <- BString("I am a BString object")
>  > d <- DNAString("TTGAAAA-CTC-N")
>
> With the first, I get this error:
>
>     Error in BString("I am a BString object") : Error in nchar(src) :
>       2 arguments passed to .Internal(nchar) which requires 3
>
> With the second, I get:
>
>     Error in DNAString("TTGAAAA-CTC-N") : Error in nchar(src) :
>       2 arguments passed to .Internal(nchar) which requires 3
>
>
> I'm running bioc 2.6; is that my problem?
>
> sessionInfo ()
> R version 2.6.0 alpha (2007-09-12 r42830)
> i386-apple-darwin8.10.1
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RUnit_0.4.17      Biostrings_2.5.19
>
> loaded via a namespace (and not attached):
> [1] tools_2.6.0
>
>
> Thanks!
>
>   - Paul
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



More information about the Bioconductor mailing list