[BioC] makePDpackage problem

[Ben Bolstad]

This is an error I have fixed in the devel branch (boils down to a
problem in affyio). If there is sufficient demand I will back-patch it
to the release branch. The bug was originally manifesting only in the
windows build, and drove me crazy for the better part of a weekend, was
basically driven by an interaction between pointer aliasing and gcc
optimization.

Best,

Ben

> My problem: When I try to run the command I get the following error.
> 
> 
> > makePDpackage("Sp20b_M_v04.bpmap", file1 = "Sp20b_M_v04.cif", manufacturer = "affymetrix",type="tiling")
> affymetrix tiling 
> The package will be called pd.sp20b.m.v04 
> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : 
>         SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> 
> My session info is as follows:
> > sessionInfo()
> R version 2.5.0 (2007-04-23) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=Norwegian (Bokml)_Norway.1252;LC_CTYPE=Norwegian (Bokml)_Norway.1252;LC_MONETARY=Norwegian (Bokml)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokml)_Norway.1252
> 
> attached base packages:
>  [1] "grid"      "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
> 
> other attached packages:
>    makePlatformDesign                 oligo BufferedMatrixMethods        BufferedMatrix               RSQLite 
>               "1.0.0"             "1.0.2-3"               "1.0.0"               "1.0.0"               "0.5-4" 
>                   DBI           tilingArray                pixmap                   vsn                 limma 
>               "0.2-3"              "1.14.0"               "0.4-7"               "2.2.0"              "2.10.0" 
>           strucchange              sandwich                   zoo          affyQCReport           geneplotter 
>               "1.3-2"               "2.0-2"               "1.3-1"              "1.14.0"              "1.14.0" 
>               lattice              annotate          RColorBrewer               affyPLM                 gcrma 
>              "0.15-8"              "1.14.1"               "0.2-3"              "1.12.0"               "2.8.0" 
>           matchprobes              affydata                xtable            simpleaffy            genefilter 
>               "1.8.1"              "1.11.2"               "1.4-6"             "2.10.11"              "1.14.1" 
>              survival                  affy                affyio               Biobase 
>                "2.31"              "1.14.0"               "1.4.0"              "1.14.0"
> 
> 
> 
> 
> 
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> 
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