[Bioc-devel] GAlignments Sorting Causes C Stack Error

[Dario Strbenac]

Good day,

When sort is used on a GAlignments object, a stack error is shown, no matter how small the object is.

> testAlignments
GAlignments object with 3 alignments and 0 metadata columns:
                                          seqnames strand       cigar    qwidth     start       end     width     njunc
                                             <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> <integer>
  700666F:126:C8768ANXX:3:2204:3175:99484    chr14      +      71S27M        98  18386040  18386066        27         0
  700666F:126:C8768ANXX:1:1107:8115:31928    chr14      +      40S60M       100  18915005  18915064        60         0
  700666F:126:C8768ANXX:1:2206:7564:34686    chr14      +      40S50M        90  18915005  18915054        50         0
  -------
  seqinfo: 23 sequences from an unspecified genome

> sort(testAlignments)
Error: C stack usage  7970544 is too close to the limit

I use up-to-date packages.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

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

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

other attached packages:
 [1] GenomicAlignments_1.10.0   Rsamtools_1.26.1           Biostrings_2.42.1          XVector_0.14.0            
 [5] SummarizedExperiment_1.4.0 Biobase_2.34.0             GenomicRanges_1.26.2       GenomeInfoDb_1.10.1       
 [9] IRanges_2.8.1              S4Vectors_0.12.1           BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
[1] lattice_0.20-34    bitops_1.0-6       grid_3.3.2         zlibbioc_1.20.0    Matrix_1.2-7.1     BiocParallel_1.8.1
[7] tools_3.3.2

--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia