I've narrowed down this bug to the R.utils package and fixed it. I've
verified that the RMA pipeline now also works running in /tmp/.
Update aroma.affymetrix (including R.utils) by running:
source("http://callr.org/install#aroma.affymetrix";)
in a fresh R session.
/Henrik
On Tue, Sep 16, 2014 at 11:11 PM, jjspring OH <sshshoh1...@gmail.com> wrote:
> Finally working well after changing into one step further deeper directory
> as your comment,
>
> Sunghee
>
>
> 2014년 9월 17일 수요일 오후 3시 2분 20초 UTC+9, Henrik Bengtsson 님의 말:
>>
>> (Back to the public forum)
>>
>> REPRODUCIBLE EXAMPLE:
>> It's a bug (still to be found) that shows itself when one runs the
>> analysis in one directory up from the root /, e.g. /arom-anal/. I
>> managed to reproduce this by running a standard analysis in /tmp/.
>>
>> WORKAROUND:
>> Run the analysis in directory that is at least one step deeper, e.g.
>> /foo/arom-anal/. The problem goes away when I run the analysis in
>> /tmp/foo/.
>>
>> Please confirm that the above workaround also works for you and thanks
>> for reporting on this. I'll fix the bug as soon as I can.
>>
>> /Henrik
>>
>> On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH <sshsh...@gmail.com> wrote:
>> >
>> >
>> > yes it is working
>> >
>> >>
>> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1")
>> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1"
>> >
>> >
>> > Sunghee
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > Sunghee Oh, PhD
>> > Director, Kim Sook Za Children's Hospital Medical Center Research
>> > Foundation,
>> > 745 JikJi Daero Heung Deok Gu
>> > Cheng Ju City Chung Buk
>> > 361-841, S. Korea
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson
>> > <h...@biostat.ucsf.edu>
>> > wrote:
>> >>
>> >> Let's continue this off the list to spare the others the noise and
>> >> post back when we found the solution.
>> >>
>> >> Continuing, and before I'll have to dig into the low-level code to
>> >> figure out why you possibly could get this weird problem, does
>> >>
>> >>
>> >> Arguments$getReadablePath("plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1")
>> >>
>> >> work as well?
>> >>
>> >> /Henrik
>> >>
>> >>
>> >>
>> >> On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH <sshsh...@gmail.com>
>> >> wrote:
>> >> >
>> >> >
>> >> >
>> >> > Hi Henrik,
>> >> >
>> >> > See the outputs:
>> >> >
>> >> >> path <- getPath(plm)
>> >> >> print(path)
>> >> > [1] "plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1"
>> >> >> dir("plmData")
>> >> > [1] "tissues,RBC,QN,RMA" "tissues,RBC,QN,RMA,merged"
>> >> >> isDirectory("plmData")
>> >> > [1] TRUE
>> >> >> Arguments$getReadablePath("plmData")
>> >> > [1] "plmData"
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > 2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:
>> >> >>
>> >> >> Ok, and then the output of:
>> >> >>
>> >> >> path <- getPath(plm)
>> >> >> print(path)
>> >> >> dir("plmData")
>> >> >> isDirectory("plmData")
>> >> >> Arguments$getReadablePath("plmData")
>> >> >>
>> >> >> /H
>> >> >>
>> >> >>
>> >> >> On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH <sshsh...@gmail.com>
>> >> >> wrote:
>> >> >> > Hi Henrik,
>> >> >> >
>> >> >> > See below:
>> >> >> >
>> >> >> >
>> >> >> >> print(plm)
>> >> >> > RmaPlm:
>> >> >> > Data set: tissues
>> >> >> > Chip type: RaGene-1_0-st-v1,r3
>> >> >> > Input tags: RBC,QN
>> >> >> > Output tags: RBC,QN,RMA
>> >> >> > Parameters: {probeModel: chr "pm", shift: num 0, flavor: chr
>> >> >> > "affyPLM",
>> >> >> > treatNAsAs: chr "weights"}
>> >> >> > Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
>> >> >> > RAM: 0.00MB
>> >> >> >> print(getwd())
>> >> >> > [1] "/arom-anal"
>> >> >> >
>> >> >> >
>> >> >> > Thanks
>> >> >> > Sunghee
>> >> >> >
>> >> >> >
>> >> >> > 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말:
>> >> >> >>
>> >> >> >> That is really odd and I've never seen that error (8-9 years
>> >> >> >> now).
>> >> >> >> There must be a simple answer to this. What does:
>> >> >> >>
>> >> >> >> print(plm)
>> >> >> >> print(getwd())
>> >> >> >>
>> >> >> >> output when you get to that step.
>> >> >> >>
>> >> >> >> /Henrik
>> >> >> >>
>> >> >> >>
>> >> >> >> On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH <sshsh...@gmail.com>
>> >> >> >> wrote:
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Hi,
>> >> >> >> >
>> >> >> >> > After setting up the directory, performed background correction
>> >> >> >> > and
>> >> >> >> > rank
>> >> >> >> > based quantile normalization,
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > library(aroma.affymetrix)
>> >> >> >> >
>> >> >> >> > verbose <- Arguments$getVerbose(-8, timestamp=T)
>> >> >> >> >
>> >> >> >> > chipType <- "RaGene-1_0-st-v1"
>> >> >> >> >
>> >> >> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>> >> >> >> >
>> >> >> >> > cs <- AffymetrixCelSet$byName("tissues",cdf=cdf)
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > print(cs)
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >> cs
>> >> >> >> > AffymetrixCelSet:
>> >> >> >> > Name: tissues
>> >> >> >> > Tags:
>> >> >> >> > Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
>> >> >> >> > Platform: Affymetrix
>> >> >> >> > Chip type: RaGene-1_0-st-v1,r3
>> >> >> >> > Number of arrays: 8
>> >> >> >> > Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1),
>> >> >> >> > CS
>> >> >> >> > _
>> >> >> >> > 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
>> >> >> >> > Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
>> >> >> >> > Total file size: 84.50MB
>> >> >> >> > RAM: 0.01MB
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > bc <- RmaBackgroundCorrection(cs)
>> >> >> >> >
>> >> >> >> > csBC <- process(bc,verbose=verbose)
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > qn <- QuantileNormalization(csBC, typesToUpdate = "pm")
>> >> >> >> >
>> >> >> >> > print(qn)
>> >> >> >> >
>> >> >> >> > csN <- process(qn, verbose = verbose)
>> >> >> >> >
>> >> >> >> > plm <- RmaPlm(csN)
>> >> >> >> >
>> >> >> >> > print(plm)
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Until here, looks fine, BUT, when i perform fit function as
>> >> >> >> > below
>> >> >> >> > and
>> >> >> >> > the
>> >> >> >> > errors come out related with directory,
>> >> >> >> >
>> >> >> >> > fit(plm, verbose = verbose)
>> >> >> >> >
>> >> >> >> > qam <- QualityAssessmentModel(plm)
>> >> >> >> >
>> >> >> >> > #plotNuse(qam)
>> >> >> >> >
>> >> >> >> > plotRle(qam)
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > current directory is /arom-anal, and setting up the data files
>> >> >> >> > (annotation,
>> >> >> >> > cel files, and raw data) look fine(see below hierarchical
>> >> >> >> > structure
>> >> >> >> > of
>> >> >> >> > directories),
>> >> >> >> > After you take a closer look at the following errors, could you
>> >> >> >> > please
>> >> >> >> > let
>> >> >> >> > me know what the problems are?
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Creating CEL file...done
>> >> >> >> > [2014-09-17 13:29:59] Exception: Pathname not found:
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
>> >> >> >> > (none of the parent directories
>> >> >> >> > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist;
>> >> >> >> > current
>> >> >> >> > directory is '/arom-anal')
>> >> >> >> >
>> >> >> >> > at #22. getReadablePathname.Arguments(static, ...)
>> >> >> >> > - getReadablePathname.Arguments() is in environment
>> >> >> >> > 'R.utils'
>> >> >> >> >
>> >> >> >> > at #21. getReadablePathname(static, ...)
>> >> >> >> > - getReadablePathname() is in environment 'R.utils'
>> >> >> >> > - originating from '<text>'
>> >> >> >> >
>> >> >> >> > at #20. Arguments$getReadablePathname(filename, path = path,
>> >> >> >> > absolutePath
>> >> >> >> > = TRUE,
>> >> >> >> > mustExist = mustExist)
>> >> >> >> > - Arguments$getReadablePathname() is local of the
>> >> >> >> > calling
>> >> >> >> > function
>> >> >> >> >
>> >> >> >> > at #19. GenericDataFile(...)
>> >> >> >> > - GenericDataFile() is in environment 'R.filesets'
>> >> >> >> >
>> >> >> >> > at #18. extend(GenericDataFile(...),
>> >> >> >> > c("AromaMicroarrayDataFile",
>> >> >> >> > uses("FileCacheKeyInterface")))
>> >> >> >> > - extend() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #17. AromaMicroarrayDataFile(...)
>> >> >> >> > - AromaMicroarrayDataFile() is in environment
>> >> >> >> > 'aroma.core'
>> >> >> >> >
>> >> >> >> > at #16. extend(AromaMicroarrayDataFile(...),
>> >> >> >> > c("AffymetrixFile",
>> >> >> >> > uses("AromaPlatformInterface")))
>> >> >> >> > - extend() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #15. AffymetrixFile(...)
>> >> >> >> > - AffymetrixFile() is in environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #14. extend(AffymetrixFile(...), "AffymetrixCelFile",
>> >> >> >> > `cached:.header`
>> >> >> >> > = NULL,
>> >> >> >> > `cached:.lastPlotData` = NULL, .cdf = NULL)
>> >> >> >> > - extend() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #13. AffymetrixCelFile(...)
>> >> >> >> > - AffymetrixCelFile() is in environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #12. extend(AffymetrixCelFile(...), c("ParameterCelFile",
>> >> >> >> > uses("ParametersInterface")),
>> >> >> >> > `cached:.readUnitsCache` = NULL, encodeFunction =
>> >> >> >> > encodeFunction,
>> >> >> >> > decodeFunction = decodeFunction)
>> >> >> >> > - extend() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #11. ParameterCelFile(...)
>> >> >> >> > - ParameterCelFile() is in environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #10. extend(ParameterCelFile(...), "ProbeAffinityFile",
>> >> >> >> > `cached:.firstCells` = NULL,
>> >> >> >> > probeModel = probeModel)
>> >> >> >> > - extend() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #09. this(...)
>> >> >> >> > - this() is in environment 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #08. newInstance.Class(.class, getPathname(paf), cdf =
>> >> >> >> > getCdf(ds),
>> >> >> >> > probeModel = this$probeModel)
>> >> >> >> > - newInstance.Class() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #07. newInstance(.class, getPathname(paf), cdf =
>> >> >> >> > getCdf(ds),
>> >> >> >> > probeModel
>> >> >> >> > = this$probeModel)
>> >> >> >> > - newInstance() is in environment 'R.oo'
>> >> >> >> >
>> >> >> >> > at #06. getProbeAffinityFile.ProbeLevelModel(this, verbose =
>> >> >> >> > less(verbose))
>> >> >> >> > - getProbeAffinityFile.ProbeLevelModel() is in
>> >> >> >> > environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #05. NextMethod("getProbeAffinityFile")
>> >> >> >> > - NextMethod() is in environment 'base'
>> >> >> >> >
>> >> >> >> > at #04. getProbeAffinityFile.RmaPlm(this, verbose =
>> >> >> >> > less(verbose))
>> >> >> >> > - getProbeAffinityFile.RmaPlm() is in environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #03. getProbeAffinityFile(this, verbose = less(verbose))
>> >> >> >> > - getProbeAffinityFile() is in environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #02. fit.ProbeLevelModel(plm, verbose = verbose)
>> >> >> >> > - fit.ProbeLevelModel() is in environment
>> >> >> >> > 'aroma.affymetrix'
>> >> >> >> >
>> >> >> >> > at #01. fit(plm, verbose = verbose)
>> >> >> >> > - fit() is in environment 'aroma.core'
>> >> >> >> >
>> >> >> >> > Error: Pathname not found:
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
>> >> >> >> > (none of the parent directories
>> >> >> >> > [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist;
>> >> >> >> > current
>> >> >> >> > directory is '/arom-anal')
>> >> >> >> > In addition: Warning messages:
>> >> >> >> > 1: In is.na(parent) :
>> >> >> >> > is.na() applied to non-(list or vector) of type 'NULL'
>> >> >> >> > 2: In is.na(parent) :
>> >> >> >> > is.na() applied to non-(list or vector) of type 'NULL'
>> >> >> >> > 20140917 13:29:59| Setting up parameter sets...done
>> >> >> >> > 20140917 13:29:59|Fitting model of class RmaPlm...done
>> >> >> >> >
>> >> >> >> > verdas-MacBook-Pro:arom-anal sungheeoh$ ls -R | grep ":$" | sed
>> >> >> >> > -e
>> >> >> >> > 's/:$//'
>> >> >> >> > -e 's/[^-][^\/]*\//--/g' -e 's/^/ /' -e 's/-/|/'
>> >> >> >> > |-annotationData
>> >> >> >> > |---chipTypes
>> >> >> >> > |-----RaGene-1_0-st-v1
>> >> >> >> > |-plmData
>> >> >> >> > |---tissues,RBC,QN,RMA
>> >> >> >> > |-----RaGene-1_0-st-v1
>> >> >> >> > |-probeData
>> >> >> >> > |---tissues,QN
>> >> >> >> > |-----RaGene-1_0-st-v1
>> >> >> >> > |---tissues,RBC
>> >> >> >> > |-----RaGene-1_0-st-v1
>> >> >> >> > |---tissues,RBC,QN
>> >> >> >> > |-----RaGene-1_0-st-v1
>> >> >> >> > |-rawData
>> >> >> >> > |---tissues
>> >> >> >> > |-----RaGene-1_0-st-v1
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >> sessionInfo()
>> >> >> >> > R version 3.1.1 (2014-07-10)
>> >> >> >> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> >> >> >> >
>> >> >> >> > locale:
>> >> >> >> > [1]
>> >> >> >> > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> >> >> >> >
>> >> >> >> > attached base packages:
>> >> >> >> > [1] parallel stats graphics grDevices utils datasets
>> >> >> >> > methods
>> >> >> >> > [8] base
>> >> >> >> >
>> >> >> >> > other attached packages:
>> >> >> >> > [1] preprocessCore_1.26.1 Biostrings_2.32.1
>> >> >> >> > XVector_0.4.0
>> >> >> >> > [4] Biobase_2.24.0 oligoClasses_1.26.0
>> >> >> >> > BiocGenerics_0.10.0
>> >> >> >> > [7] BiocInstaller_1.14.2 aroma.light_2.0.0
>> >> >> >> > matrixStats_0.10.0
>> >> >> >> > [10] aroma.affymetrix_2.12.0 aroma.core_2.12.1
>> >> >> >> > R.devices_2.11.0
>> >> >> >> > [13] R.filesets_2.6.0 R.utils_1.33.0
>> >> >> >> > R.oo_1.18.0
>> >> >> >> > [16] oligo_1.28.2 IRanges_1.22.10
>> >> >> >> > affxparser_1.36.0
>> >> >> >> > [19] R.methodsS3_1.6.1
>> >> >> >> >
>> >> >> >> > loaded via a namespace (and not attached):
>> >> >> >> > [1] affyio_1.32.0 aroma.apd_0.5.0 base64enc_0.1-2
>> >> >> >> > [4] bit_1.1-12 codetools_0.2-9 DBI_0.3.0
>> >> >> >> > [7] digest_0.6.4 DNAcopy_1.38.1 ff_2.2-13
>> >> >> >> > [10] foreach_1.4.2 GenomeInfoDb_1.0.2
>> >> >> >> > GenomicRanges_1.16.4
>> >> >> >> > [13] iterators_1.0.7 PSCBS_0.43.0 R.cache_0.10.0
>> >> >> >> > [16] R.huge_0.8.0 R.rsp_0.19.0 splines_3.1.1
>> >> >> >> > [19] stats4_3.1.1 tools_3.1.1 zlibbioc_1.10.0
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Thanks in advance!
>> >> >> >> >
>> >> >> >> > Sunghee
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > --
>> >> >> >> > 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
>> >> >> > 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
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>> >> >> > 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
>> >> > To unsubscribe and other options, go to
>> >> > http://www.aroma-project.org/forum/
>> >> >
>> >> > ---
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>> >> > 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.
>
>
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--
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