[BioC] Affy TilingArray makePDpackage
Ben Bolstad
bmb at bmbolstad.com
Wed Jun 6 06:39:37 CEST 2007
I guess this is what I get for not reading the mailing list that closely
these days (even when my name is mentioned).
I think I have fixed this issue in affyio 1.5.4, let me know if it is
still not working when ever the windows version gets built.
Best,
Ben
On Tue, 2007-06-05 at 16:14 -0700, joseph wrote:
> Has anybody figure out the solution to the following 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 2.5.0 (2007-04-23)
> i686-redhat-linux-gnu
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> attached base packages:
> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils"
> [7] "datasets" "methods" "base"
> other attached packages:
> makePlatformDesign oligo BufferedMatrixMethods
> "1.0.0" "1.0.2-3" "1.0.0"
> BufferedMatrix RSQLite DBI
> "1.0.0" "0.5-4" "0.2-3"
> Biobase affyio
> "1.14.0" "1.4.0"
>
> ----- Original Message ----
> From: James W. MacDonald <jmacdon at med.umich.edu>
> To: joseph <jdsandjd at yahoo.com>
> Cc: Bioconductor <Bioconductor at stat.math.ethz.ch>; Ben Bolstad <bmb at bmbolstad.com>
> Sent: Wednesday, May 2, 2007 10:34:25 AM
> Subject: Re: [BioC] Affy TilingArray makePDpackage
> joseph wrote:
> > Hi Jim
> > Both files are in the working directory.
> > I just tried the same thing on my Windows machine.
> I get the same result. The error occurs at the line
> bpmap <- .Call("ReadBPMAPFileIntoRList", bpmapFile, PACKAGE = "affyio")
> so it appears there is a Windows-specific problem with the C code. This
> code was written by Ben Bolstad, so I am ccing him as well.
> Best,
> Jim
> >dir()
> > [1] "Mm_PromPR_v01_NCBIv35.bpmap" "Mm_PromPR_v02.cif"
> >>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 2.5.0 (2007-04-23)
> > 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:
> > makePlatformDesign oligo BufferedMatrixMethods BufferedMatrix RSQLite
> > "1.0.0" "1.0.2" "1.0.0" "1.0.0" "0.5-3"
> > DBI Biobase affyio
> > "0.2-2" "1.14.0" "1.4.0"
> > ----- Original Message ----
>
> > From: James W. MacDonald <jmacdon at med.umich.edu>
>
> > To: joseph <jdsandjd at yahoo.com>
>
> > Cc: bioconductor at stat.math.ethz.ch
>
> > Sent: Wednesday, May 2, 2007 8:52:56 AM
>
> > Subject: Re: [BioC] Affy TilingArray makePDpackage
>
> >
>
> > Hi Joseph,
>
> >
>
> >
>
> >
>
> > joseph wrote:
>
> >
>
> >
>
> >>Hi
>
> >
>
> >
>
> >
>
> >>I upgraded to R 2.5.0 and Bioc 2.0. When I tried to build a data package
>
> >
>
> >
>
> >>for the mouse promoter tiling array, I got the following error message:
>
> >
>
> >
>
> >
>
> >> 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'
>
> >
>
> >
>
> >
>
> >
>
> > That's odd. I just successfully did the same thing:
>
> >
>
> >
>
> >
>
> > > makePDpackage(dir()[14], dir()[15], manufacturer = "affymetrix", type
>
> >
>
> > = "tiling", extra=extra)
>
> >
>
> > affymetrix tiling
>
> >
>
> > The package will be called pd.mm.prompr.v01
>
> >
>
> > Array identified as having 2166 rows and 2166 columns.
>
> >
>
> > Creating package in /home/jmacdon/Desktop/pd.mm.prompr.v01
>
> >
>
> > [1] "pd.mm.prompr.v01"
>
> >
>
> > > sessionInfo()
>
> >
>
> > R version 2.5.0 (2007-04-23)
>
> >
>
> > x86_64-unknown-linux-gnu
>
> >
>
> >
>
> >
>
> > locale:
>
> >
>
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> >
>
> >
>
> >
>
> > attached base packages:
>
> >
>
> > [1] "splines" "tools" "stats" "graphics" "grDevices" "datasets"
>
> >
>
> > [7] "utils" "methods" "base"
>
> >
>
> >
>
> >
>
> > other attached packages:
>
> >
>
> > makePlatformDesign oligo BufferedMatrixMethods
>
> >
>
> > "1.0.0" "1.0.2" "1.0.0"
>
> >
>
> > BufferedMatrix RSQLite DBI
>
> >
>
> > "1.0.0" "0.5-3" "0.2-2"
>
> >
>
> > Biobase affyio
>
> >
>
> > "1.14.0" "1.4.0"
>
> >
>
> >
>
> >
>
> > Are both of the BPMAP and CIF files in your working directory?
>
> >
>
> >
>
> >
>
> > Best,
>
> >
>
> >
>
> >
>
> > Jim
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >>>sessionInfo()
>
> >
>
> >
>
> >>R version 2.5.0 (2007-04-23)
>
> >
>
> >
>
> >>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:
>
> >
>
> >
>
> >> makePlatformDesign oligo BufferedMatrixMethods BufferedMatrix RSQLite
>
> >
>
> >
>
> >> "1.0.0" "1.0.2"
>
> >
>
> >
>
> >> "1.0.0" "1.0.0" "0.5-3"
>
> >
>
> >
>
> >> DBI Biobase affyio
>
> >
>
> >
>
> >> "0.2-2" "1.14.0" "1.4.0"
>
> >
>
> >
>
> >
>
> >>Any help or suggestions will be appreciated.
>
> >
>
> >
>
> >> Joseph
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >>__________________________________________________
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >> [[alternative HTML version deleted]]
>
> >
>
> >
>
> >
>
> >>_______________________________________________
>
> >
>
> >
>
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>
> >
>
> >
>
> >>Bioconductor at stat.math.ethz.ch
>
> >
>
> >
>
> >>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> >
>
> >
>
> >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> >
>
> >
>
> >
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> >
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> >
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> >
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>
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