Question

Sample code doesn't seem to be working on fresh install of regioneR

1

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rcavalca ▴ 140

@rcavalca-7718

Last seen 5.2 years ago

United States

Hello,

I just installed regioneR and tried to run some of the examples in the vignette but they failed. After a fresh install from Bioconductor I did:

library(regioneR)
A <- toGRanges(data.frame(chr=c("chr1", "chr1", "chr1"), start=c(20000, 50000, 100000), end=c(22000, 70000, 400000)))
randomizeRegions(A, genome="hg19")

Error in which(genome == inst_pkgs[, "provider_version"]) : error in evaluating the argument 'x' in selecting a method for function 'which': Error in `[.data.frame`(inst_pkgs, , "provider_version") : undefined columns selected

Here is my sessionInfo():

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin14.5.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] regioneR_1.2.3       BSgenome_1.38.0      rtracklayer_1.30.4  
 [4] Biostrings_2.38.4    XVector_0.10.0       GenomicRanges_1.22.4
 [7] GenomeInfoDb_1.6.3   IRanges_2.4.8        S4Vectors_0.8.11    
[10] BiocGenerics_0.16.1  memoise_1.0.0       

loaded via a namespace (and not attached):
 [1] zlibbioc_1.16.0            GenomicAlignments_1.6.3   
 [3] BiocParallel_1.4.3         tools_3.2.2               
 [5] SummarizedExperiment_1.0.2 Biobase_2.30.0            
 [7] lambda.r_1.1.7             futile.logger_1.4.1       
 [9] digest_0.6.9               futile.options_1.0.0      
[11] bitops_1.0-6               RCurl_1.95-4.8            
[13] Rsamtools_1.22.0           XML_3.98-1.4

regioner • 1.3k views

ADD COMMENT • link updated 8.0 years ago by Martin Morgan 25k • written 8.0 years ago by rcavalca ▴ 140

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As a quick update, I installed regioneR fresh on another system and tried the same code from the vignette and received the same error.

ADD REPLY • link 8.0 years ago rcavalca ▴ 140

score 1 · Accepted Answer · 2016-05-01

1

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 days ago

United States

After I run the command above, my sessionInfo() includes the BSgenome.Hsapiens.UCSC.hg19 package; I think code (in BSgenome) is assuming that at least one BSgenome package is already installed. Try installing the BSgenome*hg19 package.

ADD COMMENT • link 8.0 years ago Martin Morgan 25k

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Thanks, that was the problem. I suppose this means that BSgenome.Hsapiens.UCSC.hg19 should be a dependency. Unfortunately it's a huge dependency.

ADD REPLY • link 8.0 years ago rcavalca ▴ 140

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Hi rcavalca,

Actually BSgenome.Hsapiens.UCSC.hg19.masked is not a dependency but a suggested package. The idea is that you need at least the BSgenome for the organism you want to work with. If you want to use the mask (so no regions ends up in the centromere, for example) then you should use the ".masked" version of the package.

You are right that it's a huge dependency. We are in the process of creating a small cache of the needed data for the most frequently used genomes and include it with regioneR, so no big download is needed.

ADD REPLY • link 8.0 years ago bernatgel ▴ 150

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It's only needed if you're working on humans and a particular genome build, so it is not a dependency per se but rather a suggested package. It (or the genome for the model or semi-model organism you work on) will be used in many Bioconductor work flows, not just regioneR, so the cost is not so bad.

ADD REPLY • link 8.0 years ago Martin Morgan 25k