Solved by truly clean install, removing the OOLock package.

I have segfault when I try to load GenomicRanges from Bioconductor 3.3. I've tried reinstalling R 3.3.1 and GenomicRanges, and reinstalling required packages, but even starting afresh the segfault keeps coming. Any ideas? Thanks Edward R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help > biocLite("GenomicRanges") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). Installing package(s) ‘GenomicRanges’ trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/macosx/mavericks/contrib/3.3/GenomicRanges_1.24.2.tgz' Content type 'application/x-gzip' length 1355102 bytes (1.3 MB) ================================================== downloaded 1.3 MB The downloaded binary packages are in /var/folders/qt/mg0xqktj3cg556m3dtjf2thw0000gn/T//RtmpIHwmfE/downloaded_packages Old packages: 'R6', 'mgcv', 'survival' Update all/some/none? [a/s/n]: n > library(GenomicRanges) 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, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: colMeans, colSums, expand.grid, rowMeans, rowSums Loading required package: IRanges Loading required package: GenomeInfoDb *** caught segfault *** address 0x18, cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 5: loadNamespace(package, lib.loc) 6: doTryCatch(return(expr), name, parentenv, handler) 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 9: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 10: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}) 11: library(GenomicRanges)

Thanks Martin. As you see this was solved. No, Bioconductor didn't think any packages were out of date, I tried that first. I think the issue was a corrupt download either of GenomicRanges or a dependency, but it was difficult to fix because I had to manually delete the package files from /Library and then redownload and install clean. BiocInstaller::biocValid(), like uninstalling and reloading the packages from R directly, did not fix the problem.

(Apologies for my poor code formatting above)