NCList_find_overlaps_in_groups

[Sethupathy-Lab]

Hi,

I recently installed PEPATAC and I keep getting the same error whether I use the test sample or my own. It is looking for the NCList_find_overlaps_in_groups function, but can't find it. Here is the exact error code:

> `Rscript /home/pr46_0001/ATACseq/pepatac//pepatac/tools/PEPATAC.R anno -p genomic -i /home/pr46_0001/ATACseq/pepatac/pepatac/testtesttest/pepatatc_test/results_pipeline/test1/peak_calling_hg38/test1_peaks_normalized.narrowPeak -f /home/pr46_0001/ATACseq/pepatac/pepatac/testtesttest/pepatatc_test/results_pipeline/test1/raw/hg38_annotations.bed -g hg38 -o /home/pr46_0001/ATACseq/pepatac/pepatac/testtesttest/pepatatc_test/results_pipeline/test1/QC_hg38/test1_peak_genomic_distribution.pdf` (17653)
<pre>
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'NCList_find_overlaps_in_groups' not found
Calls: <Anonymous>
Execution halted

I thought this might be part of IRanges, but I don't see it in that library. I've attached my full log as well.

Thanks for any help you have!

PEPATAC_log.txt

[nsheff]

This is coming from GenomicRanges... are you using an old version of GenomicRanges and bioconductor? What's your R sessionInfo()?

Like:

Rscript -e "library(GenomicRanges);sessionInfo()"

[Sethupathy-Lab]

Thanks for the quick response! Below is my session info:

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /programs/R-4.0.0/lib/libRblas.so
LAPACK: /programs/R-4.0.0/lib/libRlapack.so

locale:
[1] C

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

other attached packages:
[1] GenomicRanges_1.40.0 GenomeInfoDb_1.26.2  IRanges_2.24.1
[4] S4Vectors_0.28.1     BiocGenerics_0.36.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.36.0        compiler_4.0.0         tools_4.0.0
[4] XVector_0.30.0         GenomeInfoDbData_1.2.4 RCurl_1.98-1.2
[7] bitops_1.0-6

[nsheff]

Hmm... the only thing I can think of is a version mismatch among bioconductor packages. Maybe try re-installing/updating S4Vectors, GenomicRanges, and IRanges?

I mean, can you run overlaps with GenomicRanges in general, outside pepatac?

[Sethupathy-Lab]

Thanks for your help, I re-installed everything from scratch and it is working now.

[nsheff]

Great, glad it's working. Let us know if you run into more issues.