http://www.bioconductor.org/packages/2.1/bioc/html/affyio.html On Jun 9, 2007, at 2:00 PM, joseph wrote: > 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 at="" bmbolstad.com=""> > To: joseph <jdsandjd at="" yahoo.com=""> > Cc: James W. MacDonald <jmacdon at="" med.umich.edu="">; Bioconductor > <bioconductor at="" 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",manufacture >>> r="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_U >> S.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.UT >> F-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",manufactur >>>> er="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",manufactur >>>> er="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 >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >> >> >> >> > > > > > > > > > > ______________________________________________________________________ > ______________ > > > [[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