Hey Henrik, first of all thanks for the effort and your help! As you suggested, I installed the 'fixed' future package and set future::plan to 'eager' and now receive the following message upon fit(cbs):

*Error: Something is wrong with the copy-number ratios of sample 'GSM1704973,chipEffects' relative to reference '.baseline,aa03679a3cdfd0f39ecaf0c9a2c80eeb' on chromosome 1. Too many non-finite values: 231306 (100.0% > 20.0%) out of 231306. If this is expected, you may adjust argument 'maxNAFraction' when setting up CbsModel().* So, all CN ratios are NA, right? If so, I guess the problem is upstream, perhaps in one of the normalization steps? On Saturday, July 2, 2016 at 4:46:26 AM UTC+2, Henrik Bengtsson wrote: > > 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-af...@googlegroups.com <javascript:>> 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-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. 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