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Question: tracklayer - browserSession() Infinite Recursion Error
1
gravatar for andrew.j.skelton73
2.5 years ago by
United Kingdom
andrew.j.skelton73290 wrote:

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.  

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by andrew.j.skelton73290
1
gravatar for Hervé Pagès
2.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Andrew,

I can't reproduce this:

library(rtracklayer)
session <- browserSession()
session
# A genome browser session of class 'UCSCSession' with 0 views and 178 tracks

Please provide your sessionInfo(). See mine below.

Thanks,

H.

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] rtracklayer_1.28.4   GenomicRanges_1.20.4 GenomeInfoDb_1.4.0  
[4] IRanges_2.3.10       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      
 [4] bitops_1.0-6            GenomicAlignments_1.4.1 futile.options_1.0.0   
 [7] zlibbioc_1.14.0         XVector_0.8.0           futile.logger_1.4.1    
[10] lambda.r_1.1.7          BiocParallel_1.2.2      tools_3.2.0            
[13] RCurl_1.95-4.6         
ADD COMMENTlink written 2.5 years ago by Hervé Pagès ♦♦ 13k

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! 

ADD REPLYlink written 2.5 years ago by andrew.j.skelton73290

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. 

ADD REPLYlink written 2.5 years ago by andrew.j.skelton73290

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.

ADD REPLYlink written 2.5 years ago by Michael Lawrence9.8k

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

ADD REPLYlink written 2.5 years ago by andrew.j.skelton73290

Is there a workaround for this problem? Or do I have to wait until this problem has been fixed internally?

ADD REPLYlink written 2.5 years ago by David Nieuwenhuijse0

Bug fix should be committed by now, I think. Install rtracklayer from biocLite() and it should be working. 

ADD REPLYlink written 2.5 years ago by andrew.j.skelton73290

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.

ADD REPLYlink written 2.5 years ago by David Nieuwenhuijse0

you could try the dev release to see if it was committed there... 

useDevel()

Failing that, you'll need to wait for an update from Michael Lawrence, as he's the maintainer. 

ADD REPLYlink written 2.5 years ago by andrew.j.skelton73290

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.

ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 21k
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