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 <[email protected]> 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 [email protected]
> 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 [email protected].
> 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 <[email protected]
> <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 [email protected]
> <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 [email protected] <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 [email protected]
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 [email protected].
For more options, visit https://groups.google.com/d/optout.
