I have recently starting using an old server.
We have installed AchLinux, and RStudio Server (2022.07.999 build 999) on the device. The server is running dual Xeon E5-2470 with 48GB RAM.
I'm trying to install.packages("sf") and during the installation I get the following:
** testing if installed package can be loaded from temporary location
*** caught illegal operation ***
address 0x55b94289a1e0, cause 'unknown'
Traceback:
1: CPL_gdal_init()
2: load_gdal()
3: fun(libname, pkgname)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(libname, pkgname), error = identity)
8: runHook(".onLoad", env, package.lib, package)
9: loadNamespace(package, lib.loc)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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)})
14: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
15: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
16: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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))})
21: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
22: tools:::.test_load_package("sf", "/home/trevor/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-sf/00new")
An irrecoverable exception occurred. R is aborting now ...
ERROR: loading failed
* removing ‘/home/trevor/R/x86_64-pc-linux-gnu-library/4.2/sf’
Warning in install.packages :
installation of package ‘sf’ had non-zero exit status
A similar error happens if I install.packages("rgdal").
I believe based on the above that there's an issue with the gdal package in ArchLinux, installed using pacman, we've installed all the optional parts of the package, but the errors still occur.
We have installed V3.5.0-4 of gdal as shown below:
pacman -Qi gdal
Name : gdal
Version : 3.5.0-4
Description : A translator library for raster and vector geospatial data formats
Architecture : x86_64
URL : https://gdal.org/
Licenses : custom
Groups : None
Provides : None
Depends On : proj blosc crypto++ curl libdeflate expat libfreexl geos libgeotiff giflib libjpeg-turbo
json-c xz libxml2 lz4 unixodbc ocl-icd openssl pcre2 libpng qhull libspatialite sqlite
libtiff xerces-c zlib zstd
Optional Deps : arrow: Arrow/Parquet support [installed]
cfitsio: FITS support [installed]
hdf5: HDF5 support [installed]
libheif: HEIF support [installed]
mariadb-libs: MySQL support [installed]
netcdf: netCDF support [installed]
openexr: EXR support [installed]
openjpeg2: JP2 support [installed]
podofo: PDF support [installed]
poppler: PDF support [installed]
postgresql-libs: PostgreSQL support [installed]
libwebp: WebP support [installed]
Required By : python-gdal
Optional For : None
Conflicts With : None
Replaces : None
Installed Size : 27.98 MiB
Packager : Bruno Pagani <[email protected]>
Build Date : Fri Jul 1 21:44:46 2022
Install Date : Sun Jul 24 16:22:48 2022
Install Reason : Explicitly installed
Install Script : No
Validated By : Signature
Can anyone help with this error?
The problem is the arrow package. https://github.com/apache/arrow/issues/12681
The solution: is to rebuild the arrow package manually with flags -DARROW_SIMD_LEVEL=SSE4_2 or -DARROW_SIMD_LEVEL=NONE, depending on the instructions set supported by your CPU