Good to hear. I'll fix/workaround this peculiar problem so this won't the future. It might be a while before you see the fix, but it's added to my todo list [https://github.com/HenrikBengtsson/R.oo/issues/5].

/Henrik On Mon, Jan 26, 2015 at 9:00 AM, Jerry Liu <jerry.liu2...@gmail.com> wrote: > It worked! I did load the annotation package and hgu133a for other analysis. > Couldt be some name space collision. Restarting seems to work. Now it had > passed that error and running... > > Thanks again very much! > Jerry > > On Monday, January 26, 2015 at 11:32:25 AM UTC-5, Henrik Bengtsson wrote: >> >> On Mon, Jan 26, 2015 at 7:56 AM, Jerry Liu <jerry....@gmail.com> wrote: >> > 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. >> >> I think I understand the problem(*). The immediate >> solution/workaround for you is to retry in a fresh R session such that >> there are no package already loaded, particularly not all those >> Bioconductor annotation data packages. That should do it. >> >> Henrik >> >> (*) The solution is to make the R.oo package (mine) to also handle >> deprecated setups in Bioconductor - aready too much technical details. >> >> > >> > 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....@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-af...@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-affymetr...@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> 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 >> >> > 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. >> >> > 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-af...@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-affymetr...@googlegroups.com. >> > 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. -- -- 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.