On Mon, Jan 26, 2015 at 7:56 AM, Jerry Liu <jerry.liu2...@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.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
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>> 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-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.
