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

[Paul Shannon]

Hi Herve,

I just got R-2.6 from http://r.research.att.com/#nightly and then  
Biostrings
via biocLite -- in the last few minutes.

sessionInfo is below, and here is the (strangely persistent) error  
message.  I
was sure that getting the latest build from AT&T, as Henrik  
suggested, would
do the trick!

  - Paul


library (Biostrings)
 > DNAString ('AT')
Error in DNAString("AT") : Error in nchar(src) :
   2 arguments passed to .Internal(nchar) which requires 3


R version 2.6.0 RC (2007-09-27 r43002)
i386-apple-darwin8.10.1

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biostrings_2.5.19

loaded via a namespace (and not attached):
[1] tools_2.6.0
 >


On Sep 28, 2007, at 2:19 PM, Herve Pages wrote:

> 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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>