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

[Herve Pages]

Paul Shannon wrote:
> 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!

Thanks for upating your setup and sorry that it didn't make the trick...

A really strange error indeed, but (sorry if my question is obvious) are
you sure that your nchar() is working properly? Can you please try this:

  > nchar('AT')

Otherwise, I have no idea why this call (R/BString-class.R, line 96)

  length <- nchar(src)

would produce the error you get!!? I'll need help from other Mac OS X
users: anybody else here that is able to reproduce Paul's problem?
Thanks in advance!

H.


> 
>  - 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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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>