Hi Henrik , Thanks very much for your such quick reply! It could be a Bioconductor error. I'd appreciate it greatly if you could give me some suggestions on how to fix this.
Here's the trace back: 19: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA) 18: .Defunct(msg = msg) 17: (function () { if (grepl("PFAM", x)) { bimapName <- paste0(prefix, "PFAM") } else { bimapName <- paste0(prefix, "PROSITE") } x <- dc[[bimapName]] msg = wmsg(paste0(bimapName, " is defunct. ", "Please use select() if you need access to PFAM or PROSITE accessions. \n")) if (interactive()) { .Defunct(msg = msg) } })() 16: eval(expr, envir, enclos) 15: eval(expr, envir = envir) 14: FUN(c("hgu133a", "hgu133aACCNUM", "hgu133aALIAS2PROBE", "hgu133aCHR", "hgu133aCHRLENGTHS", "hgu133aCHRLOC", "hgu133aCHRLOCEND", "hgu133a.db", "hgu133a_dbconn", "hgu133a_dbfile", "hgu133a_dbInfo", "hgu133a_dbschema", "hgu133aENSEMBL", "hgu133aENSEMBL2PROBE", "hgu133aENTREZID", "hgu133aENZYME", "hgu133aENZYME2PROBE", "hgu133aGENENAME", "hgu133aGO", "hgu133aGO2ALLPROBES", "hgu133aGO2PROBE", "hgu133aMAP", "hgu133aMAPCOUNTS", "hgu133aOMIM", "hgu133aORGANISM", "hgu133aORGPKG", "hgu133aPATH", "hgu133aPATH2PROBE", "hgu133aPFAM", "hgu133aPMID", "hgu133aPMID2PROBE", "hgu133aPROSITE", "hgu133aREFSEQ", "hgu133aSYMBOL", "hgu133aUNIGENE", "hgu133aUNIPROT")[[29L]], ...) 13: lapply(X = X, FUN = FUN, ...) 12: sapply(objectNames, FUN = function(objectName) { expr <- substitute({ is.function(x) && inherits(x, "Class") }, list(x = as.name(objectName))) eval(expr, envir = envir) }) 11: getKnownSubclassesInEnvironment(name, envir = envir) 10: getKnownSubclasses.Class(clazz) 9: getKnownSubclasses(clazz) 8: getFileListClass.GenericDataFileSetList(this) 7: getFileListClass(this) 6: getFileList.GenericDataFileSetList(cesTuple, array, ..., verbose = less(verbose, 1)) 5: getFileList(cesTuple, array, ..., verbose = less(verbose, 1)) 4: getDataFileMatrix.CopyNumberChromosomalModel(this, array = array, verbose = less(verbose, 5)) 3: getDataFileMatrix(this, array = array, verbose = less(verbose, 5)) 2: fit.CopyNumberSegmentationModel(sm, verbose = -10) 1: fit(sm, verbose = -10) On Mon, Jan 26, 2015 at 10:31 AM, Jerry Liu <jerry.liu2...@gmail.com> wrote: > Hello, > > I got an error after trying to fit the CBS model: > > Error: hgu133aPFAM is defunct. Please use select() if you > need access to PFAM or PROSITE accessions. > > Here are the command I ran: > > ds<-doCRMAv2("GSE57277_DLBCL", chipType="Mapping250K_Sty", plm="RmaCnPlm") > sm<-CbsModel(ds) > fit(sm, verbose=-10) > > I have no clue of how to use select() as per the error message to fix this > problem. My R session info is at the bottom of the email. Please help, many > thanks! > > Jerry > > > sessionInfo(): > R version 3.1.1 (2014-07-10) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices > [6] utils datasets methods base > > other attached packages: > [1] DNAcopy_1.40.0 preprocessCore_1.28.0 > [3] sfit_0.3.0 aroma.light_2.2.0 > [5] aroma.affymetrix_2.12.0 aroma.core_2.12.1 > [7] R.devices_2.12.0 R.filesets_2.6.0 > [9] R.utils_1.34.0 R.oo_1.18.0 > [11] affxparser_1.38.0 R.methodsS3_1.6.1 > [13] hgu133a.db_3.0.0 org.Hs.eg.db_3.0.0 > [15] RSQLite_1.0.0 DBI_0.3.1 > [17] gage_2.16.0 annotate_1.44.0 > [19] XML_3.98-1.1 AnnotationDbi_1.28.1 > [21] GenomeInfoDb_1.2.3 IRanges_2.0.0 > [23] S4Vectors_0.4.0 hgu133acdf_2.15.0 > [25] affy_1.44.0 Biobase_2.26.0 > [27] BiocGenerics_0.12.1 > > loaded via a namespace (and not attached): > [1] affyio_1.34.0 aroma.apd_0.5.0 > [3] base64enc_0.1-2 BiocInstaller_1.16.1 > [5] Biostrings_2.34.0 Cairo_1.5-6 > [7] digest_0.6.4 graph_1.44.0 > [9] httr_0.5 KEGGREST_1.6.1 > [11] matrixStats_0.12.2 png_0.1-7 > [13] PSCBS_0.43.0 R.cache_0.10.0 > [15] R.huge_0.8.0 R.rsp_0.19.0 > [17] splines_3.1.1 stringr_0.6.2 > [19] tools_3.1.1 xtable_1.7-4 > [21] XVector_0.6.0 zlibbioc_1.12.0 > > -- > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > On Monday, January 26, 2015 at 10:46:46 AM UTC-5, Henrik Bengtsson wrote: > > On Mon, Jan 26, 2015 at 7:31 AM, Jerry Liu <jerry....@gmail.com > <javascript:>> wrote: > > > > Hello, > > > > I got an error after trying to fit the CBS model: > > > > Error: hgu133aPFAM is defunct. Please use select() if you > > need access to PFAM or PROSITE accessions. > > > > Here are the command I ran: > > > > ds<-doCRMAv2("GSE57277_DLBCL", chipType="Mapping250K_Sty", > plm="RmaCnPlm") > > sm<-CbsModel(ds) > > fit(sm, verbose=-10) > > > > I have no clue of how to use select() as per the error message to fix > this problem. My R session info is at the bottom of the email. Please help, > many thanks! > > This does not an error message for the Aroma Framework, but more > likely something from a Bioconductor package. It's not obvious to me > how that is triggered by the above call. Could you please send what > traceback() outputs immediately after you get the error. > > /Henrik > > > > > Jerry > > > > > > sessionInfo(): > > R version 3.1.1 (2014-07-10) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats4 parallel stats graphics grDevices > > [6] utils datasets methods base > > > > other attached packages: > > [1] DNAcopy_1.40.0 preprocessCore_1.28.0 > > [3] sfit_0.3.0 aroma.light_2.2.0 > > [5] aroma.affymetrix_2.12.0 aroma.core_2.12.1 > > [7] R.devices_2.12.0 R.filesets_2.6.0 > > [9] R.utils_1.34.0 R.oo_1.18.0 > > [11] affxparser_1.38.0 R.methodsS3_1.6.1 > > [13] hgu133a.db_3.0.0 org.Hs.eg.db_3.0.0 > > [15] RSQLite_1.0.0 DBI_0.3.1 > > [17] gage_2.16.0 annotate_1.44.0 > > [19] XML_3.98-1.1 AnnotationDbi_1.28.1 > > [21] GenomeInfoDb_1.2.3 IRanges_2.0.0 > > [23] S4Vectors_0.4.0 hgu133acdf_2.15.0 > > [25] affy_1.44.0 Biobase_2.26.0 > > [27] BiocGenerics_0.12.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.34.0 aroma.apd_0.5.0 > > [3] base64enc_0.1-2 BiocInstaller_1.16.1 > > [5] Biostrings_2.34.0 Cairo_1.5-6 > > [7] digest_0.6.4 graph_1.44.0 > > [9] httr_0.5 KEGGREST_1.6.1 > > [11] matrixStats_0.12.2 png_0.1-7 > > [13] PSCBS_0.43.0 R.cache_0.10.0 > > [15] R.huge_0.8.0 R.rsp_0.19.0 > > [17] splines_3.1.1 stringr_0.6.2 > > [19] tools_3.1.1 xtable_1.7-4 > > [21] XVector_0.6.0 zlibbioc_1.12.0 > > > > -- > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > > > > You received this message because you are subscribed to the Google > Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. > > > To post to this group, send email to aroma-af...@googlegroups.com > <javascript:> > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > --- > > You received this message because you are subscribed to the Google > Groups "aroma.affymetrix" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to aroma-affymetr...@googlegroups.com <javascript:>. > > For more options, visit https://groups.google.com/d/optout. > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.