RStudio quits unexpectedly while running DiffBind on R 3.4.0
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Entering edit mode
msabbag2 • 0
@msabbag2-12954
Last seen 4.1 years ago

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

software error diffbind rstudio abort quit • 677 views
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0
Entering edit mode

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

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Entering edit mode

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

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0
Entering edit mode

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

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2
Entering edit mode
Gord Brown ▴ 630
@gord-brown-5664
Last seen 5 months ago
United Kingdom

Hi,

Based on the data you provided offline, I reproduced and (eventually...) fixed the bug (buffer overflow).  It'll show up as DiffBind 2.4.2 (or 2.5.1 in the development branch) after the next build cycle of Bioconductor (usually a day or so).

Thanks for reporting it.

Cheers,

 - Gord

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