I am trying to use distanceToNearest() to get the closest distance between two GRanges objects. The method usually works well but has been giving me an error (Error in new_Hits(Class, from, to, nLnode, nRnode, mcols) : 
  'nLnode' and 'nRnode' must be single integers) which I am not sure how to resolve. 

distanceToNearest(myRanges1, myRanges2, ignore.strand=T)
Error in new_Hits(Class, from, to, nLnode, nRnode, mcols) : 
  'nLnode' and 'nRnode' must be single integers

myRanges1

GRanges object with 5547 ranges and 0 metadata columns:
         seqnames               ranges strand
            <Rle>            <IRanges>  <Rle>
     [1]     chr1   [      0,       0]      *
     [2]     chr1   [ 300000,  300000]      *
     [3]     chr1   [ 425000,  425000]      *
     [4]     chr1   [ 800000,  800000]      *
     [5]     chr1   [1875000, 1875000]      *
     ...      ...                  ...    ...

myRanges2

GRanges object with 9535 ranges and 0 metadata columns:
         seqnames                 ranges strand
            <Rle>              <IRanges>  <Rle>
     [1]     chr1 [   825000,    825000]      *
     [2]     chr1 [144900000, 144900000]      *
     [3]     chr1 [145000000, 145000000]      *
     [4]     chr1 [145400000, 145400000]      *
     [5]     chr1 [145650000, 145650000]      *
     ...      ...                    ...    ...

Hello,

I am actually getting 2 different errors:

> distanceToNearest(myRanges1, myRanges2, ignore.strand=T)
Error in new_Hits(Class, from, to, nLnode, nRnode, mcols) : 
  'nLnode' and 'nRnode' must be single integers

> distanceToNearest(myRanges3, myRanges4, ignore.strand=T)
Error in rep(seq(lx)[v], w) : invalid 'times' argument

I have attached objects myRanges1 to myRanges4, as well as my R session. Nothing looks unusual about these ranges. Also, some ranges combinations fail but work fine if combined with other ranges. 

Thanks!

Rola

## TO DOWNLOAD: press on the "myRanges" link, NOT on the "Download" button which pops up an ad. 

I tested the links; 

Rsession:

http://s000.tinyupload.com/?file_id=07521718617224259851

Ranges1:4

http://s000.tinyupload.com/?file_id=00421462498421829601

http://s000.tinyupload.com/?file_id=04242812352144597405

http://s000.tinyupload.com/?file_id=70020862917644622055

 http://s000.tinyupload.com/?file_id=06464838747515157530

Here is my session info in case that is helpful:

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

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

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

other attached packages:
[1] reshape_0.8.5        stringr_1.1.0        ggplot2_2.1.0        GenomicRanges_1.24.2 GenomeInfoDb_1.8.5  
[6] IRanges_2.6.1        S4Vectors_0.10.3     BiocGenerics_0.18.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.6      grid_3.3.0       plyr_1.8.4       gtable_0.2.0     magrittr_1.5     scales_0.4.0    
 [7] stringi_1.1.1    zlibbioc_1.18.0  XVector_0.12.1   tools_3.3.0      munsell_0.4.3    colorspace_1.2-6

When I do it, on my mac I get a different error:

distanceToNearest(myRanges1, myRanges2)
Error in .Call2("Hits_new", queryHits, subjectHits, queryLength, subjectLength,  : 
  'subjectHits' must contain non-NA values >= 1 and <= 'subjectLength'

I have figured out what triggers one of the errors but not the other:

distanceToNearest(myRanges3, myRanges4, ignore.strand=T)
Error in rep(seq(lx)[v], w) : invalid 'times' argument

seems to be triggered by ranges that start at 0. if I remove all the ranges that start at zero, the error is not triggered. 

FYI, when adding information to your question use 'ADD COMMENT' or 'edit' instead of posting an answer to your own question.

Thanks for sending the files. This was a bug in the follow() method for GenomicRanges. distanceToNearest() calls both proceed() and follow() and was failing because of the problems in follow(). I've checked in a fix to GenomicRanges 1.24.3 in release and 1.25.94 in devel. Both should be available via biocLite() Saturday after noon PST or immediately from svn.

Thanks for reporting the bug. Let us know if you have any other problems.

Valerie