Also, install the following version of the future package:
source("http://callr.org/install#HenrikBengtsson/future@FutureErrorFix";)
This should reveal the true underlying error message.
/Henrik
On Friday, July 1, 2016 at 11:09:36 AM UTC-7, Henrik Bengtsson wrote:
>
> 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
> >> > 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/
> >
> > ---
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> > To unsubscribe from this group and stop receiving emails from it, send
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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
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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