Hello!

I have a set of genome-wide interactions (gi1). I then subset these interactions to one chromosome and used the anchors to generate new interactions (gi2). My problem now is I want to see which of the new interactions I made were in the original genome-wide set, but since gi1 contains regions from all chromosomes, it has many more ranges than gi2, and R Studio crashes when I try to compare the 2 sets.

Through some testing, I have realized that when 2 GInteractions objects have different ranges in their regions, using either gi1 %in% gi2 or findOverlaps(gi1, gi2) crashes my RStudio session with the "R Session Aborted. R encountered a fatal error." popup.

Here is a simple example that causes the error:

library(InteractionSet)

## Setup modified from the example constructor for GInteractions
# Create first GInteractions object
N <- 30
all.starts <- sample(1000, N)
all.ends <- all.starts + round(runif(N, 5, 20))
all.regions <- GRanges(rep(c("chrA", "chrB"), c(N-10, 10)), IRanges(all.starts, all.ends))

Np <- 20
all.anchor1 <- sample(N, Np)
all.anchor2 <- sample(N, Np)
gi1 <- GInteractions(all.anchor1, all.anchor2, all.regions)

# re-sample to get new ranges
all.starts <- sample(1000, N)
all.ends <- all.starts + round(runif(N, 5, 20))
all.regions <- GRanges(rep(c("chrA", "chrB"), c(N-10, 10)), IRanges(all.starts, all.ends))

all.anchor1 <- sample(N, Np)
all.anchor2 <- sample(N, Np)
gi2 <- GInteractions(all.anchor1, all.anchor2, all.regions)

## Compare interactions
## This line crashes my RStudio session
gi1 %in% gi2

## Alternatively, this line also crashes my RStudio session
findOverlaps(gi1, gi2)

I've run this simple example just using R on the command line and got the following traceback:

 *** caught bus error ***
address 0x100000cfeedfacf, cause 'invalid alignment'

Traceback:
 1: .paired_overlap_finder2(query, subject, select = select, maxgap = maxgap,     minoverlap = minoverlap, type = type, ignore.strand = ignore.strand,     ..., use.region = use.region)
 2: .local(query, subject, maxgap, minoverlap, type, select, ...)
 3: findOverlaps(x, table, type = "equal", select = "first", use.region = "same")
 4: findOverlaps(x, table, type = "equal", select = "first", use.region = "same")
 5: match(x, table, nomatch = 0L)
 6: match(x, table, nomatch = 0L)
 7: gi1 %in% gi2
 8: gi1 %in% gi2

My session info:

> sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] InteractionSet_1.30.0       SummarizedExperiment_1.32.0
 [3] Biobase_2.62.0              MatrixGenerics_1.14.0      
 [5] matrixStats_1.2.0           GenomicRanges_1.54.1       
 [7] GenomeInfoDb_1.38.5         IRanges_2.36.0             
 [9] S4Vectors_0.40.2            BiocGenerics_0.48.1        

loaded via a namespace (and not attached):
 [1] SparseArray_1.2.3       zlibbioc_1.48.0         Matrix_1.6-5           
 [4] lattice_0.22-5          abind_1.4-5             GenomeInfoDbData_1.2.11
 [7] S4Arrays_1.2.0          XVector_0.42.0          RCurl_1.98-1.14        
[10] bitops_1.0-7            grid_4.3.2              DelayedArray_0.28.0    
[13] compiler_4.3.2          tools_4.3.2             Rcpp_1.0.12            
[16] crayon_1.5.2

Any help/advice would be appreciated!

Hm. Smells like an issue with the C++ code in InteractionSet, though I don't see any issues running it on my own computer (Ubuntu Linux, R-devel). Nothing comes up with valgrind, either.

Perhaps you could debug(InteractionSet:::.paired_overlap_finder2) and confirm exactly where it crashes. The primary suspect would be the .Call to cxx_paired_olaps.