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

[Herve Pages]

Hi Paul,

Here are 2 things that you could check:

  - How did you install R-2.6? Did you compile it yourself or did you use
    the universal binary from the "R for Mac OS X Developer's Page":

      http://r.research.att.com/

    This is where we grab the R that we use on pitt (our Mac OS X build machine).

  - How did you install Biostrings? Again, did you compile it yourself (with
    e.g. biocLite("Biostrings", type="source")), or are you using our
    universal binary. You'll get our binary with

      biocLite("Biostrings", type="mac.binary")

    or just

      biocLite("Biostrings")

    if you didn't change the "pkgType" option in your startup file.

There are many different ways to configure and install things from source
on Mac OS X and there is no way for us to test our packages for all the
possible setups. So when someone chooses this path, s/he is more or less
on his/her own because we have no way to reproduce their problem. Sorry!

Please test again but with the latest universal binary from the "R for Mac
OS X Developer's Page" and with biocLite("Biostrings", type="mac.binary")
and let us know if you still have this problem. Thanks!

H.


Paul Shannon 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
> 
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