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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.ci f",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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald Affymetrix and cDNA Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Please don't take things off-list. We view the list archives as a useful source of information. I have re-sent to the list, but I don't know how to make Thunderbird respect the threading so this will appear as a new thread which is sub-optimal. 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.ci f",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_U S.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 at stat.math.ethz.ch > > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.