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/
---
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