Issues running hdf5r and re-installing it

[CJ1017]

Hi, I'm running into issues when running a command that uses hdf5r, the command was working fine a couple of months ago but now is crashing R and causing the following error:

loom<- read.loom.matrices("GBM035_M.loom") reading loom file via hdf5r...

• caught illegal operation * address 0x2b9a79c5a123, cause 'illegal operand'

Traceback: 1: fun(libname, pkgname) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch(fun(libname, pkgname), error = identity) 6: runHook(".onLoad", env, package.lib, package) 7: loadNamespace(name) 8: getNamespace(ns) 9: asNamespace(ns) 10: getExportedValue(pkg, name) 11: hdf5r::H5File 12: read.loom.matrices("GBM035_M.loom")

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 1 R is aborting now ... Illegal instruction”

I then uninstalled hdf5r and tried to install, however when I tried to re-install, I got a similar error:

** testing if installed package can be loaded from temporary location sh: line 1: 66446 Illegal instruction '/software/apps/R/3.6.1/gcc/5.5.0/lib64/R/bin/R' --no-save --slave 2>&1 < '/tmp/RtmpBHccwj/filefff36e4edd38'

• caught illegal operation * address 0x2ae8374e7123, cause 'illegal operand'

Traceback: 1: fun(libname, pkgname) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch(fun(libname, pkgname), error = identity) 6: runHook(".onLoad", env, package.lib, package) 7: loadNamespace(package, lib.loc) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, 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)}) 12: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) 13: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage")) 14: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)) 15: doTryCatch(return(expr), name, parentenv, handler) 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17: tryCatchList(expr, classes, parentenv, handlers) 18: 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 sm <- strsplit(conditionMessage(e), "\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 && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 19: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))) 20: tools:::.test_load_package("hdf5r", "/home-net/home-1//R/x86_64-pc-linux-gnu-library/3.6/gcc/5.5/00LOCK-hdf5r/00new") An irrecoverable exception occurred. R is aborting now ... ERROR: loading failed

• removing ‘/home-net/home-1/R/x86_64-pc-linux-gnu-library/3.6/gcc/5.5/hdf5r’

The downloaded source packages are in ‘/tmp/RtmpDGnuKT/downloaded_packages’ Warning message: In install.packages("hdf5r") : installation of package ‘hdf5r’ had non-zero exit status

Would appreciate any help.

[hhoeflin]

Sorry, I have not seen this error before.