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I am running a pipeline that uses R on terminal to run a script:

R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.3

I suddenly get this error. I have checked other users errors and tried to uninstall and install the packages using

ip <- installed.packages() pkgs.to.remove <- ip[!(ip[,"Priority"] %in% c("base", "recommended")), 1] sapply(pkgs.to.remove, remove.packages)

but it does not work and I keep having the same error. Could you give me a hand trying to guess how I could fix this?

many thanks

EC

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:

 1: dyn.load(file, DLLpath = DLLpath, ...)

 2: library.dynam(lib, package, package.lib)

 3: loadNamespace(package, lib.loc)

 4: doTryCatch(return(expr), name, parentenv, handler)

 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])

 6: tryCatchList(expr, classes, parentenv, handlers)

 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})

8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)

 9: .getRequiredPackages2(pkgInfo, quietly = quietly)

10: library(DESeq2)

11: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))

12: suppressPackageStartupMessages({    library(DESeq2)})

An irrecoverable exception occurred. R is aborting now ...

'Rscript /Users/user1/samsa2/R_scripts/run_DESeq_stats.R -I /Volumes/ECG_WORK/JC150_T0/results/step_5_output/RefSeq_results/org_results -O RefSeq_org_DESeq_results.tab -R /Volumes/ECG_WORK/JC150_T0/results/step_2_output/raw_counts.txt' exited with non-zero status 139
Ecg
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    Do you get the error when you try to remove the packages? It's not clear what you're trying to do. You should include a [mcve] of the code you're running that gives the error. – divibisan Feb 21 '19 at 20:00
  • Apologies @divibisan The error comes when I run my script as of bash script.sh I have seen online it is to do with different R versions installed and packages being out dated, so they recommend uninstalling all the packages on R and re-install them. Which is what I successfully did, but then I keep having the same error when running my script again. – Ecg Feb 22 '19 at 14:39

0 Answers0