Hi,
Building
R-4.2.1-foss-2022a.EasyBuild
fails with a segfault on my CentOS 7.9 system in the testing step for
the package
Rmpi
with the following error:
sh: line 1: 187847 Segmentation fault R_TESTS=
'/trinity/shared/easybuild/software/R/4.2.1-foss-2022a/lib64/R/bin/R' --no-save
--no-restore --no-echo 2>&1 <
'/scratch/eb-build/eb-py6glg1h/RtmpteVB5y/file2d2f97c3a6e53'
*** caught segfault ***
address 0x41f0002ddc7, cause 'unknown'
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 && !quietly)
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)
tryInvokeRestart("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, nlines = 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("Rmpi",
"/trinity/shared/easybuild/software/R/4.2.1-foss-2022a/lib64/R/library/00LOCK-Rmpi/00new")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
Any ideas what might be happening?
Cheers,
Loris
--
Dr. Loris Bennett (Herr/Mr)
ZEDAT, Freie Universität Berlin
