[BioC] mu11ksuba + gcrma = error

[Ido M. Tamir]

Hi,
similar to others 
(http://thread.gmane.org/gmane.science.biology.informatics.conductor/18693)
I have to report an error with GCRMA (2.12.1). 
The other package I normally use ATM ("mouse4302") works fine in this
setup.
I also removed the mu11ksubacdf and mu11ksuba probes package and 
installed an older version (2.0.0) manually, but this also did not help.

thank you very much,
ido


>    raw <- 
ReadAffy(filenames=paste("cel/",pData(ad)$fileName,sep=""),phenoData=ad)
>    eset <- gcrma(raw,fast=FALSE)
trying 
URL 'http://bioconductor.org/packages/2.2/data/annotation/src/contrib/mu11ksubacdf_2.2.0.tar.gz'
Content type 'application/x-gzip' length 437563 bytes (427 Kb)
opened URL
==================================================
downloaded 427 Kb

* Installing *source* package 'mu11ksubacdf' ...
** R
** data
** help
 >>> Building/Updating help pages for package 'mu11ksubacdf'
     Formats: text html latex example 
  geometry                          text    html    latex   example
  mu11ksubacdf                      text    html    latex
  mu11ksubadim                      text    html    latex
** building package indices ...
* DONE (mu11ksubacdf)

The downloaded packages are in
	/tmp/RtmpCmPqvz/downloaded_packages
Adjusting for optical effect............Done.
Computing affinities[1] "Checking to see if your internet connection works..."
trying 
URL 'http://bioconductor.org/packages/2.2/data/annotation/src/contrib/mu11ksubaprobe_2.2.0.tar.gz'
Content type 'application/x-gzip' length 1191866 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 Mb

* Installing *source* package 'mu11ksubaprobe' ...
** R
** data
** help
 >>> Building/Updating help pages for package 'mu11ksubaprobe'
     Formats: text html latex example 
  mu11ksubaprobe                    text    html    latex   example
** building package indices ...
* DONE (mu11ksubaprobe)

The downloaded packages are in
	/tmp/RtmpCmPqvz/downloaded_packages
.Done.
Adjusting for non-specific binding.Error in pms[, i] <- GSB.adj(Yin = pms[, 
i], subset = index.affinities,  : 
  number of items to replace is not a multiple of replacement length
>    eset <- gcrma(raw,fast=FALSE)
Adjusting for optical effect............Done.
Computing affinities.Done.
Adjusting for non-specific binding.Error in pms[, i] <- GSB.adj(Yin = pms[, 
i], subset = index.affinities,  : 
  number of items to replace is not a multiple of replacement length
> package.version("gcrma")
[1] "2.12.1"
> traceback()
3: gcrma.engine(pms = pm(object), mms = mm(object), ncs, pm.affinities = 
pm(affinity.info), 
       mm.affinities = mm(affinity.info), anc, type = type, k = k, 
       stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, 
       rho = rho, verbose = verbose, fast = fast)
2: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = 
affinity.source, 
       NCprobe = NCprobe, type = type, k = k, stretch = stretch, 
       correction = correction, GSB.adjust = GSB.adjust, rho = rho, 
       optical.correct = optical.correct, verbose = verbose, fast = fast)
1: gcrma(raw, fast = FALSE)
>