I'm running into a small problem creating the PD package for the bee. It is
looking for geometry info, but I can't seem to add it.
The package is created with no error, and the XYS files seem to load, but
returns: Error in geometry(get(pkgname)) :
  no slot of name "geometry" for this object of class "platformDesign"

### constructing package

> library(makePlatformDesign)
Loading required package: affyio
Loading required package: oligo
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
>
makePDpackage("~/Bee_Project/ApisMel4_JHpkns_AF_meth_HX1.ndf","~/Bee_Project/Bee_XYS/247194_635.xys","~/Bee_Project/ApisMel4_JHpkns_AF_meth_HX1.pos",manufacturer="nimblegen",type="tiling",ncol=14
00,nrow=1050)
Error in makePDpackage("~/Bee_Project/ApisMel4_JHpkns_AF_meth_HX1.ndf",  :
  unused argument(s) (ncol = 1400, nrow = 1050)
>
makePDpackage("~/Bee_Project/ApisMel4_JHpkns_AF_meth_HX1.ndf","~/Bee_Project/Bee_XYS/247194_635.xys","~/Bee_Project/ApisMel4_JHpkns_AF_meth_HX1.pos",manufacturer="nimblegen",type="tiling")
nimblegen tiling
The package will be called pd.apismel4.jhpkns.af.meth.hx1
Reading ~/Bee_Project/ApisMel4_JHpkns_AF_meth_HX1.ndf
Assuming a simple design (NOT multiple-wells).
Correcting probe positions... Done.
Creating package in /home/bst/other/bherb/pd.apismel4.jhpkns.af.meth.hx1
[1] "pd.apismel4.jhpkns.af.meth.hx1"

### Installing package

[bherb@compute-0-43 ~]$ R CMD INSTALL -l ~/bin/R-devel/library
~/pd.apismel4.jhpkns.af.meth.hx1
* Installing *source* package 'pd.apismel4.jhpkns.af.meth.hx1' ...
** R
** data
** help
chmod: cannot access
`/home/bst/other/bherb/bin/R-devel/library/pd.apismel4.jhpkns.af.meth.hx1/man/pd.apismel4.jhpkns.af.meth.hx1.Rd.gz':
No such file or directory
 >>> Building/Updating help pages for package
'pd.apismel4.jhpkns.af.meth.hx1'
     Formats: text html latex example
** building package indices ...
Warning in max.default(numeric(0), na.rm = FALSE) :
  no non-missing arguments to max; returning -Inf
* DONE (pd.apismel4.jhpkns.af.meth.hx1)


### reading XYS files - based on Preprocessing script - uses read.xysfiles
command

> source("~/Bee_Project/PreprocessingBee.R")
Loading required package: lattice
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: survival
Loading required package: splines
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: affxparser
Loading required package: oligoClasses
oligo Package - Series 1.5.x

Attaching package: 'oligo'


        The following object(s) are masked from package:affy :

         list.celfiles,
         MAplot,
         mm,
         mm<-,
         mmindex,
         pm,
         pm<-,
         pmindex,
         probeNames,
         rma

Loading required package: pd.apismel4.jhpkns.af.meth.hx1
Platform design info loaded.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
. Done.
Error in geometry(get(pkgname)) :
  no slot of name "geometry" for this object of class "platformDesign"
> traceback()
6: geometry(get(pkgname))
5: geometry(get(pkgname))
4: read.xysfiles(file.path(datapath, pd$Filename), verbose = TRUE,
       phenoData = new("AnnotatedDataFrame", data = pd))
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("~/Bee_Project/PreprocessingBee.R")
> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-03-30 r44996)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C

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

other attached packages:
 [1] pd.apismel4.jhpkns.af.meth.hx1_1.5.0 oligo_1.5.6

 [3] oligoClasses_1.3.4                   affxparser_1.13.3

 [5] geneplotter_1.19.4                   annotate_1.19.2

 [7] xtable_1.5-2                         AnnotationDbi_1.3.8

 [9] RSQLite_0.6-9                        DBI_0.2-4

[11] genefilter_1.21.3                    survival_2.34-1

[13] vsn_3.7.6                            limma_2.15.9

[15] affy_1.19.4                          preprocessCore_1.3.2

[17] affyio_1.9.0                         Biobase_2.1.7

[19] lattice_0.17-10

loaded via a namespace (and not attached):
[1] grid_2.8.0         KernSmooth_2.22-22 RColorBrewer_1.0-2

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