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/ > > > > --- > > 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.