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
> <javascript:>> 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
> <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!
> >>
> >> 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.
> >
> >
> >
> > 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
> <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/
---
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