[Bioc-devel] GIntervalTree objects are corrupted during save/load

The difference of course being that you implemented those trees from
scratch, while we're relying on the Kent library for the low-level
management of the tree. We would probably need to break from the Kent
library to pursue this approach.

On Tue, Jul 1, 2014 at 9:05 AM, Herv? Pag?s <hpages at fhcrc.org
<mailto:hpages at fhcrc.org>> wrote:

    Hi Hector, Michael,


    On 07/01/2014 05:57 AM, Michael Lawrence wrote:

        It seems tough to make this work. There is no way for the R
        serialization
        machinery to understand what needs to be serialized after the
        external
        pointer. The easiest approach to fixing this would be to reimplement
        everything on top of SEXPs, which is to say, it would not be easy.


    This is what I did with PDict objects to store the Aho-Corasick tree.
    It's actually easier than it sounds. You can use any atomic type, say
    INTSXP or RAWSXP, it doesn't matter, That's just a way to get memory.
    Then you do what you want with it (thru casting the pointer to it).
    It not only solves the serialization problem, it also automatically
    manages the memory, which is now in the hands of the garbage collector.

    Cheers,
    H.

        Alternatively, we could write our own serializer. It seems R
        needs a way to
        register (de)serializers for external pointers.


        On Tue, Jul 1, 2014 at 5:37 AM, Hector Corrada Bravo
        <hcorrada at gmail.com <mailto:hcorrada at gmail.com>>
        wrote:

            Confirmed. Will look into it now.
            Thanks for writing!
            Hector


            On Tue, Jul 1, 2014 at 2:40 AM, Kristoffer Vitting-Seerup <
            kristoffer.vittingseerup at bio.__ku.dk
            <mailto:kristoffer.vittingseerup at bio.ku.dk>> wrote:

                Hi bioc-devel

                I???ve fond an error in the usage of GIntervalTree:


                    test <- GRanges(seqnames='Chr1',
                    range=IRanges(start=10,end=20)__)
                    test

                GRanges with 1 range and 0 metadata columns:
                        seqnames    ranges strand
                           <Rle> <IRanges>  <Rle>
                    [1]     Chr1  [10, 20]      *

                this object I can save and load without problem:

                save(test, file='test.Rdata')

                    rm(test)
                    load('test.Rdata')
                    test

                GRanges with 1 range and 0 metadata columns:
                        seqnames    ranges strand
                           <Rle> <IRanges>  <Rle>
                    [1]     Chr1  [10, 20]      *


                But if I convert to to a GIntervalTree (for faster
                overlap finding) I get
                a fatal error when loading:

                test2 <- GIntervalTree(test)

                    test2

                GIntervalTree with 1 range and 0 metadata columns:
                        seqnames    ranges strand
                           <Rle> <IRanges>  <Rle>
                    [1]     Chr1  [10, 20]      *

                    save(test2, file='test2.Rdata')
                    rm(test2)
                    load('test2.Rdata')
                    test2

                GIntervalTree with 1 range and 0 metadata columns:

                   *** caught segfault ***
                address 0xc, cause 'memory not mapped'

                Traceback:
                   1: .Call(.NAME, ..., PACKAGE = PACKAGE)
                   2: .Call2(fun, object at ptr, ..., PACKAGE = "IRanges")
                   3: .IntervalForestCall(from, "asIRanges")
                   4: asMethod(object)
                   5: as(x at ranges, "IRanges")
                   6: .GT_reorderValue(x, as(x at ranges, "IRanges"))
                   7: .local(x, ...)
                   8: ranges(x)
                   9: ranges(x)

                Possible actions:
                1: abort (with core dump, if enabled)
                2: normal R exit
                3: exit R without saving workspace
                4: exit R saving workspace


                My session info:
                sessionInfo()
                R version 3.1.0 (2014-04-10)
                Platform: x86_64-apple-darwin10.8.0 (64-bit)

                locale:
                [1] C

                attached base packages:
                [1] grDevices datasets  grid      parallel  stats
                graphics  utils
                methods   base

                other attached packages:
                   [1] spliceR_1.5.0         plyr_1.8.1
                  RColorBrewer_1.0-5
                   VennDiagram_1.6.5     cummeRbund_2.7.1      Gviz_1.9.4
                   rtracklayer_1.25.8    GenomicRanges_1.17.14
                GenomeInfoDb_1.1.5
                   IRanges_1.99.13
                [11] S4Vectors_0.0.6       fastcluster_1.1.13
                  reshape2_1.4
                   ggplot2_0.9.3.1       RSQLite_0.11.4        DBI_0.2-7
                BiocGenerics_0.11.2

                loaded via a namespace (and not attached):
                   [1] AnnotationDbi_1.27.6     BBmisc_1.6
                BSgenome_1.33.5
                       BatchJobs_1.2            Biobase_2.25.0
                BiocParallel_0.7.0
                      Biostrings_2.33.8        Formula_1.1-1
                   GenomicAlignments_1.1.10
                [10] GenomicFeatures_1.17.6   Hmisc_3.14-4
                MASS_7.3-33
                       R.methodsS3_1.6.1        RCurl_1.95-4.1
                Rcpp_0.11.1
                       Rsamtools_1.17.14        VariantAnnotation_1.11.5
                XML_3.98-1.1
                [19] XVector_0.5.6            biomaRt_2.21.0
                biovizBase_1.13.7
                       bitops_1.0-6             brew_1.0-6
                cluster_1.15.2
                      codetools_0.2-8          colorspace_1.2-4
                dichromat_2.0-0
                [28] digest_0.6.4             fail_1.2
                foreach_1.4.2
                       gtable_0.1.2             iterators_1.0.7
                  lattice_0.20-29
                       latticeExtra_0.6-26      matrixStats_0.8.14
                munsell_0.4.2
                [37] proto_0.3-10             scales_0.2.4
                sendmailR_1.1-2
                       splines_3.1.0            stats4_3.1.0
                stringr_0.6.2
                       survival_2.37-7          tools_3.1.0
                  zlibbioc_1.11.1



                --
                Kindest regards
                Kristoffer Vitting-Seerup, cand.scient. (M.Sc.),
                Ph.D Fellow
                Sandelin Group

                Bioinformatics Centre | Biotech Research & Innovation
                Centre (BRIC), Dep.
                Of Biology
                University of Copenhagen
                Building 1, 3th floor, office 3 (1-3-03)
                Ole Maal??es Vej 5

                DK-2200 Copenhagen N
                Denmark
                http://binf.ku.dk | http://www.bric.ku.dk







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