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_P roject/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_P roject/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_COLLA TE=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=e n_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 [[alternative HTML version deleted]]