session <- browserSession()
I get an error when trying to start a browser session. This has only appeared within the last couple of weeks and I've not been able to get around it.
The error is below - Infinite recursion.
Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)? Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)? Error in unique(unlist(lapply(dots, methods:::.class1))) : error in evaluating the argument 'x' in selecting a method for function 'unique': evaluation nested too deeply: infinite recursion / options(expressions=)? Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)?
Any suggestions? I've tried passing "UCSC" as a parameter, and I get the same error.
Cheers,
EDIT - Session Info and walk through
> library(rtracklayer) Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: GenomeInfoDb
> sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.2 LTS locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.28.4 GenomicRanges_1.20.4 GenomeInfoDb_1.4.0 IRanges_2.2.3 S4Vectors_0.6.0 BiocGenerics_0.14.0 loaded via a namespace (and not attached): [1] XML_3.98-1.2 Rsamtools_1.20.4 Biostrings_2.36.1 bitops_1.0-6 GenomicAlignments_1.4.1 futile.options_1.0.0 zlibbioc_1.14.0 [8] XVector_0.8.0 futile.logger_1.4.1 lambda.r_1.1.7 BiocParallel_1.2.2 tools_3.2.0 RCurl_1.95-4.6
> session <- browserSession() Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)? Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)? Error in unique(unlist(lapply(dots, methods:::.class1))) : error in evaluating the argument 'x' in selecting a method for function 'unique': evaluation nested too deeply: infinite recursion / options(expressions=)? Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)?
EDIT2: I uninstalled R, RStudio, deleted all libraries, then reinstalled rtracklayer from scratch. It made no difference and I get the same error.
EDIT3: Installed things on a fresh Windows installation, on a completely different network, and I'm still getting the same error. I'm pretty stumped now, so I'd appreciate any input from the developers, or anyone that has any suggestions.
Hi, thanks for your response! I forgot I've been doing package development and have development packages installed. My version of rtracklayer is 1.29.7
Any suggestion to reverse the effect of useDevel() would be welcome!
I've edited the post and added in my sessionInfo. I've tried this on 6 different machines now, all independent and I'm getting the same behaviour.
This is just because you're in Europe. UCSC changed their redirect strategy, so things break in Europe now. If someone in Europe could help me debug this, that would be great.
I'll happily help you out with any debugging needed. My email address is andrew.skelton[at]ncl.ac.uk if you'd like to contact me on there
Is there a workaround for this problem? Or do I have to wait until this problem has been fixed internally?
Bug fix should be committed by now, I think. Install rtracklayer from biocLite() and it should be working.
I have updated rtracklayer today, but I still have problems accessing UCSC. My problem is similar to Gviz IdeogramTrack Hsapiens/Mmusculus error. I get the same infinite recursion error as mentioned there when trying to open a browserSession directly.
you could try the dev release to see if it was committed there...
Failing that, you'll need to wait for an update from Michael Lawrence, as he's the maintainer.
I believe that the fix is working its way through the build system and, all being well, will be available after about noon, Seattle time, 17 June.