Unfortunately, there's a "bug" in future 1.0.0 causing the actual
error to be disguised as "Cannot get static instance. ..."; there
should really be an informative error message, cf.
https://github.com/HenrikBengtsson/future/issues/83.
But your traceback gives some more information and I see you're using
parallel processing, i.e. you're using:
plan(multiprocess)
somewhere at the beginning of your script, correct? As a starter,
could you retry with:
plan(eager)
If that works / doesn't work, at least it'll give some more clues
what's going on.
In the meanwhile, I'll try to fix that future bug causing us not to
see the actual error message. When I've got a working fix, I'll share
a early-access version with you.
/Henrik
On Fri, Jul 1, 2016 at 8:02 AM, roman.hillje via aroma.affymetrix
<aroma-affymetrix@googlegroups.com> wrote:
> 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> 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
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>> > "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/
>> >
>> > ---
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>> > 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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--
--
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
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