Has there been a recent update to IRanges and/or ShortRead? A script which was working fine before is now causing my R session to crash with a segfault error. The crash happens when I try to use sread() and vmatchPattern().
Thanks for the code. A somewhat simpler example is
library(Biostrings)
f1 <- system.file("extdata", "someORF.fa", package="Biostrings")
vmatchPattern("GG", readDNAStringSet(f1))
Unfortunately, it looks like there was a bug introduced in IRanges 2.4.2 but fixed in 2.4.3, which should be available via biocLite() tomorrow (Thursday) after about 3pm Eastern.
Hi Martin,
I am still getting the same error for IRanges_2.4.6
getSeq(BSgenome.Hsapiens.UCSC.hg19,"chr7") Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains NAs or out-of-bounds indices sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.1 (Yosemite) 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] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.38.0 rtracklayer_1.30.1 [4] Biostrings_2.38.3 XVector_0.10.0 BiocInstaller_1.20.1 [7] ggplot2_2.0.0 tidyr_0.3.1 dplyr_0.4.3 [10] GenomicInteractions_1.4.1 GenomicRanges_1.22.2 GenomeInfoDb_1.6.1 [13] IRanges_2.4.6 S4Vectors_0.8.5 BiocGenerics_0.16.1 loaded via a namespace (and not attached): [1] SummarizedExperiment_1.0.2 VariantAnnotation_1.16.4 reshape2_1.4.1 [4] splines_3.2.2 lattice_0.20-33 colorspace_1.2-6 [7] GenomicFeatures_1.22.7 chron_2.3-47 survival_2.38-3 [10] XML_3.98-1.3 foreign_0.8-66 DBI_0.3.1 [13] BiocParallel_1.4.3 RColorBrewer_1.1-2 lambda.r_1.1.7 [16] matrixStats_0.50.1 plyr_1.8.3 stringr_1.0.0 [19] zlibbioc_1.16.0 munsell_0.4.2 gtable_0.1.2 [22] futile.logger_1.4.1 labeling_0.3 latticeExtra_0.6-26 [25] Biobase_2.30.0 biomaRt_2.26.1 AnnotationDbi_1.32.3 [28] proto_0.3-10 Rcpp_0.12.2 acepack_1.3-3.3 [31] scales_0.3.0 Hmisc_3.17-1 Gviz_1.14.0 [34] Rsamtools_1.22.0 gridExtra_2.0.0 digest_0.6.8 [37] stringi_1.0-1 biovizBase_1.18.0 grid_3.2.2 [40] tools_3.2.2 bitops_1.0-6 magrittr_1.5 [43] lazyeval_0.1.10 RCurl_1.95-4.7 RSQLite_1.0.0 [46] dichromat_2.0-0 Formula_1.2-1 cluster_2.0.3 [49] futile.options_1.0.0 MASS_7.3-45 data.table_1.9.6 [52] assertthat_0.1 R6_2.1.1 rpart_4.1-10 [55] igraph_1.0.1 GenomicAlignments_1.6.1 nnet_7.3-11
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version 2.3.6
Please provide a reproducible example (or at least a minimal script) and the output of
sessionInfo()(after loading ShortRead and IRanges); be sure that your packages are up-to-date for the release of Bioconductor you are using, viaBiocInstaller::biocValid().Sorry! Realized I should have done that right after I hit post. It looks like sread() first fails. Then running vmatchPattern() to look for a segment within rfa causes my session to crash.
Example:
rm(list=ls()); source("http://bioconductor.org/biocLite.R"); biocLite(ask=FALSE); library('ShortRead'); sessionInfo() f1 <- system.file("extdata", "someORF.fa", package="Biostrings") rfa <- readFasta(f1) sread(rfa) vmatchPattern('GC',sread(rfa))Output:
> sessionInfo()R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)
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] stats4 parallel stats graphics
[5] grDevices utils datasets methods
[9] base
other attached packages:[1] ShortRead_1.28.0
[2] GenomicAlignments_1.6.1
[3] SummarizedExperiment_1.0.1
[4] Biobase_2.30.0
[5] Rsamtools_1.22.0
[6] GenomicRanges_1.22.1
[7] GenomeInfoDb_1.6.1
[8] Biostrings_2.38.1
[9] XVector_0.10.0
[10] IRanges_2.4.2
[11] S4Vectors_0.8.3
[12] BiocParallel_1.4.0
[13] BiocGenerics_0.16.1
[14] BiocInstaller_1.20.1
loaded via a namespace (and not attached):[1] zlibbioc_1.16.0 lattice_0.20-33
[3] hwriter_1.3.2 tools_3.2.2
[5] grid_3.2.2 latticeExtra_0.6-26
[7] lambda.r_1.1.7 futile.logger_1.4.1
[9] RColorBrewer_1.1-2 futile.options_1.0.0
[11] bitops_1.0-6
> sread(rfa)A DNAStringSet instance of length 7
width seq
Error in x@pool[[x@ranges@group[i]]] : invalid subscript
> vmatchPattern('GC',sread(rfa))*** caught segfault ***address 0x30, cause 'memory not mapped'
Traceback:1: .Call(.NAME, ..., PACKAGE = PACKAGE)
2: .Call2("XStringSet_vmatch_pattern", pattern, subject, max.mismatch, min.mismatch, with.indels, fixed, algo, ifelse(count.only, "MATCHES_AS_COUNTS", "MATCHES_AS_ENDS"), PACKAGE = "Biostrings")
3: .XStringSet.vmatchPattern(pattern, subject, max.mismatch, min.mismatch, with.indels, fixed, algorithm)
4: .local(pattern, subject, max.mismatch, min.mismatch, with.indels, fixed, algorithm, ...)
5: vmatchPattern("GC", sread(rfa))
6: vmatchPattern("GC", sread(rfa))
Possible actions:1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace