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 >>> >>> _______________________________________________ >>> 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 >> >

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)? > > _______________________________________________ > 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 >