Hi,

I am a macOS user. I am using the shell terminal to run a bash script from a pipeline, the script is linked to an R script, and when I run it I get the error below. From what I could figure out, the problem seems to be that R crashes/breaks when it is trying to load the library(S4Vectors) package. I have installed that package as stated on https://bioconductor.org/packages/release/bioc/html/S4Vectors.html and seemed to be fine. I have also uninstalled all R/R studio versions and installed the latest one, and did the same with all R packages, but I still ave the same error. Has anybody seen this before, or could give me a hand with this? Thanks,

Elena

Working directory is  /Volumes/ECG_WORK/JC150_T0/results/step_5_output/RefSeq_results/org_results 
Loading required package: S4Vectors
Loading required package: stats4
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, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, 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, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min

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

I'll start an answer, since we're getting closer. I'm not sure what you mean by 'mac terminal' versus 'R console', but...

make: *** [/Users/ecg1g15/miniconda3/envs/py2/lib/R/etc/Makeconf:167: RcppExport

suggests that you have used a conda environment to install some packages. Now you are using 'standard' R. Mixing these two installation mechanisms is causing problems, and the solution is to pick one and stick with it. I don't know how to 'undo' the mixed installation.

Personally, I would use 'standard' R, downloading and installing R from https://r-project.org and installing packages using BiocManager::install(). By default, the macOS installs the 'binary' version of packages, so most packages will install without problem.

If you were to opt instead for conda, then I think instructions like those at https://support.bioconductor.org/p/118241/#118265 will work. The conda approach is probably easier in the short term, but limited in the long term (e.g., when you want to install a package that is not in conda). I don't have direct experience with conda.

I'm also not sure about the difference between 'mac terminal' and 'R console'; I suspect that one has set environment variables (e.g., RLIBSUSER and .libPaths()) differently than the other. Again I'm not sure how to debug this remotely, but maybe the general notion of different environment variables helps.