[BioC] mas5 update.default problem

[David Ruau]

Hi Seth,
I still have the same error unfortunately.
I don't have the last gcc (gcc-4.0.1) install yet but I don't think  
that's the problem...
Do you know another program using this method update()? maybe I can  
more information for debugging.

Here is what I did:
I cleaned the entire /Library/Frameworks/R.framework/Versions/2.5/ 
Resources/library/
then I re-installed R binary, modified my .Rprofile to install from  
source.
And in R:
source("http://bioconductor.org/biocLite.R")
biocLite()
update.packages(repos=biocReposList())
# it re-install VR; affy; cluster; lattice; mgcv; nlme; rcompgen;  
simpleaffy; xtable
everything went fine...
I re-launched R and I have the same error...

 > da.26may <- ReadAffy(celfile.path="./CEL_files/")
 > da.26may.mas5 <- mas5(da.26may, sc=300)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
12625 ids to be processed
|                    |
|Error in update.default(pbt) : need an object with call component
In addition: Warning message:
$ operator not defined for this S4 class, returning NULL in: object$call

 > sessionInfo()
R version 2.5.0 (2007-04-23)
i386-apple-darwin8.9.1

locale:
C

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

other attached packages:
hgu95av2cdf        affy      affyio     Biobase
    "1.16.0"    "1.14.1"     "1.4.0"    "1.14.0"

On May 29, 2007, at 4:46 AM, Seth Falcon wrote:

> David Ruau <David.Ruau at rwth-aachen.de> writes:
>> verbose=FALSE or TRUE doesn't change anything
>> and example(mas5) give the same error...
>> I re-install the last R-patched from source nothing changed, I
>> install in despair R binary and I am still having the same problem.
>
> Hmm, how have you been instaling Biocondcutor packages?
>
> If you are using a source built R, I recommend (removing all possibly
> stale BioC packages and then):
>
>   source("http://bioconductor.org/biocLite.R")
>   biocLite("somePkg", type="source")
>
> After getting a good install, you can update like this:
>
>   library("Biobase")
>   update.packages(repos=biocReposList())
>
> If you are using the CRAN binary R, then you want type="mac.binary"
> which is the default on OSX.  I run OS X on my laptop, but use a
> source-built R.  I have the following in ~/.Rprofile:
>
>    options(repos="http://cran.fhcrc.org")
>    options(pkgType="source")
>    options(browser="open")
>
>    if (TRUE && interactive()) {
>    tryCatch({
>        source("http://bioconductor.org/biocLite.R")
>    }, error=function(e) invisible(NULL),
>             warning=function(w) cat("Not connected to the net\n"))
>    }
>
> Setting the pkgType option to "source" means I can call biocLite()
> without remember to ask for source packages.
>
>> Can I re-install update.default() method manually?
>
> No, the problem is not exactly a wrong definition.  I'm not yet
> convinced it is a problem in the software and suspect that you have a
> bad mix of versions.  Let's see if we can sort that out first.
>
> + seth
>
> -- 
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer  
> Research Center
> http://bioconductor.org
>