It's a bug in rtracklayer and is fixed in the devel branch.

Michael

On Fri, Feb 3, 2012 at 3:31 PM, Cook, Malcolm <MEC@stowers.org> wrote:

> Hi,
>
> I'm not sure whether to address this to BioConductor project or the UCSC.
>
> I am on occasion receiving the following error
>
> error "Too many pushAbortHandlers, can only handle 11"
>
> while exporting bedGraph/bigWig using rtracklayer from Bioconductor using
> the rtracklayer
>
> I see that this is coming from the errabort module of jim Kent, which I
> assume rtracklayer is wrapping/invoking.
>
> it seems intermittent or usage related, so it is difficult to fully
> characterize.
>
> The same call to export will fail, and then succeed, after restarting R.
>
> Any advice for sleuthing/correcting/workingAround much appreciated.
>
> Cheers,
>
> Malcolm Cook
> Computational Biology - Stowers Institute for Medical Research
>
>
>
>
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] tools     splines   stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] reshape_0.8.4         plyr_1.7.1            gtools_2.6.2
>  [4] log4r_0.1-3           testthat_0.6          vwr_0.1
>  [7] latticeExtra_0.6-19   RColorBrewer_1.0-5    lattice_0.20-0
> [10] RecordLinkage_0.4-1   ffbase_0.2-1          ff_2.2-5
> [13] bit_1.1-8             RSQLite_0.11.1        evd_2.2-6
> [16] ipred_0.8-11          nnet_7.3-1            survival_2.36-10
> [19] mlbench_2.1-0         MASS_7.3-16           ada_2.0-2
> [22] rpart_3.1-51          e1071_1.6             class_7.3-3
> [25] XLConnect_0.1-7       XLConnectJars_0.1-3   rJava_0.9-3
> [28] data.table_1.7.9      BSgenome_1.22.0       rtracklayer_1.14.4
> [31] RCurl_1.9-5           bitops_1.0-4.1        Rsamtools_1.6.3
> [34] Biostrings_2.22.0     GenomicFeatures_1.6.7 AnnotationDbi_1.16.11
> [37] Biobase_2.14.0        GenomicRanges_1.6.6   IRanges_1.12.5
> [40] compare_0.2-3         svUnit_0.7-5          doMC_1.2.3
> [43] multicore_0.1-7       foreach_1.3.2         codetools_0.2-8
> [46] iterators_1.0.5       ggplot2_0.9.0         stringr_0.6
> [49] sqldf_0.4-6.1         chron_2.3-42          gsubfn_0.5-7
> [52] proto_0.3-9.2         DBI_0.2-5             functional_0.1
>
> loaded via a namespace (and not attached):
>  [1] RSQLite.extfuns_0.0.1 XML_3.9-4             biomaRt_2.10.0
>  [4] colorspace_1.1-1      dichromat_1.2-4       digest_0.5.1
>  [7] evaluate_0.4.1        grid_2.14.0           memoise_0.1
> [10] munsell_0.3           reshape2_1.2.1        scales_0.1.0
> [13] zlibbioc_1.0.0
>

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