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
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