Hi Ben
Is there a way for me to get affyio 1.5.4 now or I have to wait to the next BioC release?
Thanks
Joseph

----- Original Message ----
From: Ben Bolstad <bmb@bmbolstad.com>
To: joseph <jdsandjd@yahoo.com>
Cc: James W. MacDonald <jmacdon@med.umich.edu>; Bioconductor <Bioconductor@stat.math.ethz.ch>
Sent: Tuesday, June 5, 2007 9:39:37 PM
Subject: Re: [BioC] Affy TilingArray makePDpackage

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@med.umich.edu>
> To: joseph <jdsandjd@yahoo.com>
> Cc: Bioconductor <Bioconductor@stat.math.ethz.ch>; Ben Bolstad <bmb@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@med.umich.edu>
> 
> > To: joseph <jdsandjd@yahoo.com>
> 
> > Cc: bioconductor@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]]
> 
> > 
> 
> > 
> 
> > 
> 
> >>_______________________________________________
> 
> > 
> 
> > 
> 
> >>Bioconductor mailing list
> 
> > 
> 
> > 
> 
> >>Bioconductor@stat.math.ethz.ch
> 
> > 
> 
> > 
> 
> >>https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> > 
> 
> > 
> 
> >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> 
> 
> 
> 








       
____________________________________________________________________________________


	[[alternative HTML version deleted]]

