tracklayer - browserSession() Infinite Recursion Error
1
1
Entering edit mode
@andrewjskelton73-7074
Last seen 21 months ago
United Kingdom

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.  

rtracklayer ucsc • 1.7k views
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1
Entering edit mode
@herve-pages-1542
Last seen 2 days ago
Seattle, WA, United States

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         
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0
Entering edit mode

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! 

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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. 

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0
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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.

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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

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

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0
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Bug fix should be committed by now, I think. Install rtracklayer from biocLite() and it should be working. 

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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.

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Entering edit mode

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. 

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Entering edit mode

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.

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