Thanks for the comment. Unfortunately, the error persists even after the
updates. Here is the sessionInfo() output:
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.46.0 aroma.light_3.2.0 aroma.affymetrix_3.0.0
[4] aroma.core_3.0.0 R.devices_2.14.0 R.filesets_2.10.0
[7] R.utils_2.3.0 R.oo_1.20.0 affxparser_1.44.0
[10] R.methodsS3_1.7.1 sfit_0.3.0
loaded via a namespace (and not attached):
[1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_1.0.0
[5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.3.0
[9] R.cache_0.12.0 parallel_3.3.0 base64enc_0.1-3
aroma.apd_0.6.0
[13] R.rsp_0.30.0 globals_0.6.1
I tried running fit(cbs) - which I'm sure is the same getRegions() would do
ultimately. Here are the error messages and the traceback:
fit(cbs)
*Attaching package: ‘future’*
*The following object is masked from ‘package:R.utils’:*
* %<-%*
*Attaching package: ‘future’*
*The following object is masked from ‘package:R.utils’:*
* %<-%*
*Attaching package: ‘future’*
*The following object is masked from ‘package:R.utils’:*
* %<-%*
*Attaching package: ‘future’*
*The following object is masked from ‘package:R.utils’:*
* %<-%*
*Attaching package: ‘future’*
*The following object is masked from ‘package:R.utils’:*
* %<-%*
*Error in getStaticInstance.Object(this) : *
* Cannot get static instance. Failed to locate Class object for class
'FutureError'.*
*traceback:*
24: stop("Cannot get static instance. Failed to locate Class object for
class '",
className, "'.")
23: getStaticInstance.Object(this)
22: getStaticInstance(this)
21: .getStaticInstance(this, static = static)
20: `$.Object`(c, "message")
19: c$message
18: conditionMessage.condition(cond)
17: conditionMessage(cond)
16: stop(FutureError(value, future = future))
15: value.Future(future)
14: NextMethod("value")
13: value.MulticoreFuture(future)
12: value(future)
11: eval(expr, envir, enclos)
10: eval(quote({
value <- value(future)
rm(list = future_name, envir = assign.env)
value
}), new.env())
9: eval(expr, envir, enclos)
8: eval(expr, p)
7: eval.parent(substitute(eval(quote(expr), envir)))
6: local({
value <- value(future)
rm(list = future_name, envir = assign.env)
value
})
5: mget(vars[ok], envir = x, inherits = FALSE)
4: as.list.listenv(res)
3: as.list(res)
2: fit.CopyNumberSegmentationModel(cbs)
1: fit(cbs)
I think it's pretty obvious that simply the xdr-files are missing, I just
don't know why.
On Friday, July 1, 2016 at 4:34:22 PM UTC+2, Henrik Bengtsson wrote:
>
> Quick comment: Make sure all your packages are up-to-date and retry.
> If that doesn't work, please post your sessionInfo() after you get the
> error.
>
> /Henrik
>
> On Wed, Jun 29, 2016 at 1:32 AM, roman.hillje via aroma.affymetrix
> <aroma-af...@googlegroups.com <javascript:>> wrote:
> > Hi,
> >
> > I'm currently trying to set up the analysis of CytoScanHD arrays through
> the
> > aroma pipeline but ran into an issue with the CbsModel function. I
> prepared
> > my sample and reference set so that I end up with this:
> >
> > sample set:
> >
> > CnChipEffectSet:
> >
> > Name: GSE69632
> >
> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
> >
> > Path: plmData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
> >
> > Platform: Affymetrix
> >
> > Chip type: CytoScanHD_Array,monocell
> >
> > Number of arrays: 5
> >
> > Names: GSM1704973, GSM1704988, GSM1704989, GSM1704990, GSM1704991 [5]
> >
> > Time period: 2016-06-27 14:51:08 -- 2016-06-27 14:51:11
> >
> > Total file size: 173.14MB
> >
> > RAM: 0.01MB
> >
> > Parameters: {}
> >
> >
> > reference set:
> >
> >
> > CnChipEffectSet:
> >
> > Name: referenceSet
> >
> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
> >
> > Path: plmData/referenceSet,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
> >
> > Platform: Affymetrix
> >
> > Chip type: CytoScanHD_Array,monocell
> >
> > Number of arrays: 5
> >
> > Names: .baseline, .baseline, .baseline, .baseline, .baseline [5]
> >
> > Time period: 2016-06-28 12:05:09 -- 2016-06-28 12:05:09
> >
> > Total file size: 173.14MB
> >
> > RAM: 0.01MB
> >
> > Parameters: {}
> >
> >
> > Then I do 'cbs <- CbsModel(sampleSet, referenceSet)' and get the
> following
> > output:
> >
> >
> > CbsModel:
> >
> > Name: GSE69632
> >
> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B,paired
> >
> > Chip type (virtual): CytoScanHD_Array
> >
> > Path:
> cbsData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B,paired/CytoScanHD_Array
> >
> > Number of chip types: 1
> >
> > Sample & reference file pairs:
> >
> > Chip type #1 ('CytoScanHD_Array') of 1:
> >
> > Sample data set:
> >
> > CnChipEffectSet:
> >
> > Name: GSE69632
> >
> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
> >
> > Path: plmData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
> >
> > Platform: Affymetrix
> >
> > Chip type: CytoScanHD_Array,monocell
> >
> > Number of arrays: 5
> >
> > Names: GSM1704973, GSM1704988, GSM1704989, GSM1704990, GSM1704991 [5]
> >
> > Time period: 2016-06-27 14:51:08 -- 2016-06-27 14:51:11
> >
> > Total file size: 173.14MB
> >
> > RAM: 0.01MB
> >
> > Parameters: {}
> >
> > Reference data set/file:
> >
> > CnChipEffectSet:
> >
> > Name: referenceSet
> >
> > Tags: ACC,ra,-XY,BPN,-XY,RMA,A+B
> >
> > Path: plmData/referenceSet,ACC,ra,-XY,BPN,-XY,RMA,A+B/CytoScanHD_Array
> >
> > Platform: Affymetrix
> >
> > Chip type: CytoScanHD_Array,monocell
> >
> > Number of arrays: 5
> >
> > Names: .baseline, .baseline, .baseline, .baseline, .baseline [5]
> >
> > Time period: 2016-06-28 12:05:09 -- 2016-06-28 12:05:09
> >
> > Total file size: 173.14MB
> >
> > RAM: 0.01MB
> >
> > Parameters: {}
> >
> > RAM: 0.00MB
> >
> >
> > Until here everything is fine, but when trying to run getRegions() on
> the
> > CbsModel I receive an error:
> >
> >
> > reg <- getRegions(cbs, arrays=1, chromosomes=1:22,
> > verbose=Arguments$getVerbose(-1))
> >
> > Extracting regions from all fits...
> >
> > Obtaining CN model fits (or fit if missing)...
> >
> > Error in getStaticInstance.Object(this) :
> >
> > Cannot get static instance. Failed to locate Class object for class
> > 'FutureError'.
> >
> > Obtaining CN model fits (or fit if missing)...done
> >
> > Extracting regions from all fits...done
> >
> >
> > Does anybody know what the issue could be? I suspect it has to do with
> the
> > CbsModel because the respective folder
> > (cbsData/GSE69632,ACC,ra,-XY,BPN,-XY,RMA,A+B,paired/CytoScanHD_Array)
> stays
> > empty even though attempted to be modified at the time of running the
> > getRegions command.
> >
> >
> > I would really appreciate input/feedback/ideas since I'm relatively new
> to
> > the topic :)
> >
> > --
> > --
> > 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/
---
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.
