ArchLinux服务器RStudio Server安装sf包时GDAL触发非法操作求助

环境信息 #

• 服务器配置：双Xeon E5-2470处理器、48GB内存
• 系统：ArchLinux
• R环境：RStudio Server（2022.07.999 build 999）

错误详情 #

执行install.packages("sf")时出现非法操作错误，R直接终止，错误日志如下：

** 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

执行install.packages("rgdal")时出现类似错误。

当前GDAL配置 #

已通过pacman安装GDAL 3.5.0-4，且所有可选依赖均已安装，包信息如下：

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 <archange@archlinux.org>
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

1. 降级GDAL版本 #

ArchLinux的GDAL包更新较快，3.5.0-4可能和当前R的sf/rgdal版本存在兼容性问题。可以尝试降级到更稳定的版本：

• 从Arch Linux Archive中下载旧版本的GDAL包（比如3.4.x系列）
• 执行pacman -U /path/to/gdal-old-version.pkg.tar.zst进行降级
• 降级后重新运行install.packages("sf")

2. 从源码编译安装时指定GDAL路径 #

如果降级GDAL不可行，可手动编译安装R包，强制指定系统GDAL的路径：

install.packages("sf", configure.args = c("--with-gdal-config=/usr/bin/gdal-config", "--with-proj-include=/usr/include/proj", "--with-proj-lib=/usr/lib"))

或者先安装rgdal：

install.packages("rgdal", configure.args = "--with-gdal-config=/usr/bin/gdal-config")

3. 检查CPU指令集兼容性 #

Xeon E5-2470是Sandy Bridge架构，部分新编译的GDAL包可能使用了该CPU不支持的指令集（比如AVX2）。可通过以下命令检查：

objdump -d /usr/bin/gdalinfo | grep -i avx

如果发现AVX2等指令，说明包编译时启用了不兼容的优化，需要重新编译GDAL并禁用这些指令，或使用兼容旧CPU的预编译包。

4. 更新系统和R环境 #

确保系统处于最新状态：

pacman -Syu

同时更新R到最新版本，再尝试安装sf包。

内容的提问来源于stack exchange，提问作者Trevor