I recently updated R to 3.4.0 and RStudio to 1.0.143. After doing so, I noticed that when I try to read in a peakset using DiffBind, RStudio will quit unexpectedly.
The command that causes the quit:
peakset = dba(sampleSheet = "expinfo.csv")
The output of sessionInfo() just prior to running the command that causes the quit:
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DiffBind_2.4.1 SummarizedExperiment_1.6.0 DelayedArray_0.2.0 matrixStats_0.52.2
[5] Biobase_2.36.0 GenomicRanges_1.28.0 GenomeInfoDb_1.12.0 IRanges_2.10.0
[9] S4Vectors_0.14.0 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] edgeR_3.18.0 splines_3.4.0 gtools_3.5.0 assertthat_0.2.0
[5] latticeExtra_0.6-28 amap_0.8-14 RBGL_1.52.0 GenomeInfoDbData_0.99.0
[9] Rsamtools_1.28.0 ggrepel_0.6.5 Category_2.42.0 RSQLite_1.1-2
[13] backports_1.0.5 lattice_0.20-35 limma_3.32.2 digest_0.6.12
[17] RColorBrewer_1.1-2 XVector_0.16.0 checkmate_1.8.2 colorspace_1.3-2
[21] Matrix_1.2-10 plyr_1.8.4 GSEABase_1.38.0 XML_3.98-1.7
[25] pheatmap_1.0.8 ShortRead_1.34.0 biomaRt_2.32.0 genefilter_1.58.0
[29] zlibbioc_1.22.0 xtable_1.8-2 GO.db_3.4.1 scales_0.4.1
[33] brew_1.0-6 gdata_2.17.0 BiocParallel_1.10.0 tibble_1.3.0
[37] annotate_1.54.0 ggplot2_2.2.1 GenomicFeatures_1.28.0 lazyeval_0.2.0
[41] survival_2.41-3 magrittr_1.5 memoise_1.1.0 systemPipeR_1.10.0
[45] fail_1.3 gplots_3.0.1 hwriter_1.3.2 GOstats_2.42.0
[49] graph_1.54.0 tools_3.4.0 BBmisc_1.11 stringr_1.2.0
[53] sendmailR_1.2-1 munsell_0.4.3 locfit_1.5-9.1 AnnotationDbi_1.38.0
[57] Biostrings_2.44.0 compiler_3.4.0 caTools_1.17.1 grid_3.4.0
[61] RCurl_1.95-4.8 rjson_0.2.15 AnnotationForge_1.18.0 bitops_1.0-6
[65] base64enc_0.1-3 gtable_0.2.0 DBI_0.6-1 R6_2.2.0
[69] GenomicAlignments_1.12.0 dplyr_0.5.0 rtracklayer_1.36.0 KernSmooth_2.23-15
[73] stringi_1.1.5 BatchJobs_1.6 Rcpp_0.12.10
If I run R directly in terminal, the peaksets get loaded. However, when I try to derive a consensus set of peaks by running :
consensus = dba.peakset(peakset, consensus=-DBA_REPLICATE)
I get this error message:
*** caught segfault ***
address 0x1159e1000, cause 'memory not mapped'
Traceback:
1: .Call("DiffBind_mergeScores", PACKAGE = "DiffBind", sMerged, sScore, sPeaks)
2: mergeScores(merged, def, peakset)
3: pv.merge(allpeaks, peaks, pv$class)
4: pv.vectors(tmp, minOverlap = minOverlap)
5: pv.consensus(pv, samples, sampID = sampid, minOverlap = minOverlap)
6: pv.consensusSets(pv, peaks = peaks, minOverlap = minOverlap, attributes = consensus, tissue, factor, condition, treatment, replicate, control, peak.caller, readBam, controlBam)
7: pv.peakset(DBA, peaks = peaks, sampID = sampID, tissue = tissue, factor = factor, condition = condition, treatment = treatment, replicate = replicate, control = control, peak.caller = peak.caller, peak.format = peak.format, reads = reads, consensus = consensus, readBam = bamReads, controlBam = bamControl, scoreCol = scoreCol, bLowerScoreBetter = bLowerScoreBetter, bRemoveM = bRemoveM, bRemoveRandom = bRemoveRandom, minOverlap = minOverlap, filter = filter, counts = counts)
8: dba.peakset(peakset, consensus = -DBA_REPLICATE)
Any help would be much appreciated.
Thanks,
Mark
Hi,
I can't reproduce this on R 3.4.0 (MacOS 10.10.5). (Haven't tried within RStudio due to some configuration issues.) Could you pass along to me a zip or tarball with your sample sheet and peaks files (don't need the bams)? Via dropbox, email, or whatever (email addr on DiffBind's home page).
- Gord
Hi,
FYI, I tried from within RStudio as well, and on our test data set, got no errors. So I'd be very interested to see your data.
Cheers,
- Gord
Hi Gord,
Will send data as a zip file through email. I tried the same command on another computer running R 3.3.2, and it works just fine. It was working previously on my computer, so I tried reinstalling R 3.3.3 on my computer and repeating the command. However, it still won't work which is odd.
Thanks for the help,
Mark