Entering edit mode
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
