I hope someone can help with this. You will see by my lack of providing the appropriate information necessary for you to actually diagnose this (ie, error logs) that I am an R noob. Please point me to the correct logs and I will happily provide them!
The edgeR function processAmplicons is causing R (rstudio Version 0.98.978 ) to crash. I have it working with a normal number of reads (20 million) and a small hairpin table (200 hairpins is no problem) but it crashes if I feed it my whole hairpin list of ~120,000. It generally (but not always) reports:
-- Number of Barcodes : 4 -- Number of Hairpins : 119461
Then it sits indefinitely and eventually reports the following (see below) and restarts. Usually this coincides with me clicking to another tab or something in chrome but I have let it go uninterrupted for 8+ hours with no progress. 200 hairpins takes about a minute to process and reports at the completion of each 10million reads. 120,000 hairpins will not process no matter how small i make the data set and never reports progress, just hanging after or during reading in the hairpins.
21 May 2015 20:29:15 [rsession-*****] ERROR session hadabend; LOGGED FROM: core::Error<unnamed>::rInit(const r::session::RInitInfo&) /root/rstudio/src/cpp/session/SessionMain.cpp:1694
Session info added 21:37 EDT
R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  C attached base packages: character(0) other attached packages:  edgeR_3.8.6 loaded via a namespace (and not attached):  Rcpp_0.11.3 base_3.1.1 colorspace_1.2-4 datasets_3.1.1 grDevices_3.1.1  graphics_3.1.1 limma_3.22.7 methods_3.1.1 stats_3.1.1 tools_3.1.1  utils_3.1.1