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 <[email protected]> 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
