[BioC] makePDpackage problem

[Ben Bolstad]

All well and good, except that affyio 1.5.4 doesn't have the necessary
fix and affyio 1.5.6 does.

In any case I have patched the fix to the release branch affyio, and
that will appear in the builds on the web in the next few days. It is
better not to mix and match packages from the devel and release branches
if you don't know what you are doing and don't want to suffer the
potential consequences (ie potentially even more things broken)

Best,

Ben




On Thu, 2007-06-21 at 08:33 -0700, joseph wrote:
> I tried that and I still get the same error:
> >makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif",manufacturer="affymetrix", type="tiling")
> affymetrix tiling 
> The package will be called pd.mm.prompr.v01.ncbiv35 
> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : 
>   SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
> > sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-06-09 r41897) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     
> other attached packages:
> [1] makePlatformDesign_1.1.1    oligo_0.99.98               BufferedMatrixMethods_1.1.2 BufferedMatrix_1.1.1       
> [5] RSQLite_0.5-4               DBI_0.2-3                   Biobase_1.15.14             affyio_1.5.4               
> > 
> 
> 
> ----- Original Message ----
> From: Ingrid H. G. stensen <Ingrid.H.G.Ostensen at rr-research.no>
> To: Ben Bolstad <bmb at bmbolstad.com>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Wednesday, June 20, 2007 11:42:40 PM
> Subject: Re: [BioC] makePDpackage problem
> 
> 
> 
> Hi
> 
> Thanks for the help, but I am still a bit confused.
> 
> Do I have to install the dev. version of Bioconuctor to be able to make this work?
> 
> The arrays were given to me by the peoples at the lab to check if there is any thing on the arrays and the quality of the results. Is there some other way to do this?
> 
> Regards,
> Ingrid
> 
> 
> 
> 
> 
> 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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