Problem installing ‘sf’ & 'units' package in R/4.4.2

Fabien.Cottier · November 10, 2025, 1:24pm

Primary informations

Username: $cottierf
Cluster: $bamboo

Description

Hello. I am trying to install the packages sf, and its dependencies “units” on R/4.4.2

When I trying to run the command, I am running into the error, below. Spefically, when attempting to load the package after built, R throws a *** caught illegal operation ***
address 0x15004256bc0d, cause illegal operand error. No sure what is going wrong…

Steps to Reproduce

module load GCC/13.3.0 OpenMPI/5.0.3 GEOS/3.12.2 GDAL/3.10.0 PROJ/9.4.1 CMake/3.29.3 UDUNITS/2.2.26 R/4.4.2

R

install.packages(“sf”)

Expected Result

The R sf packages includes the critical dependency R “units” should install correctly. However, it fails (see error message below and sessionInfo() outputs at the bottom).

Actual Results

Error message received, when installing R dependency package “units” (depends on system library udunits2):

trying URL ‘https://stat.ethz.ch/CRAN/src/contrib/units_1.0-0.tar.gz’
Content type ‘application/x-gzip’ length 367179 bytes (358 KB)

downloaded 358 KB

trying URL ‘https://stat.ethz.ch/CRAN/src/contrib/sf_1.0-22.tar.gz’
Content type ‘application/x-gzip’ length 9874803 bytes (9.4 MB)

downloaded 9.4 MB

installing source package ‘units’ …
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 1.0-0
checking for default C++ standard… 201703
checking whether the C++ compiler works… yes
checking for C++ compiler default output file name… a.out
checking for suffix of executables…
checking whether we are cross compiling… no
checking for suffix of object files… o
checking whether the compiler supports GNU C++… yes
checking whether g++ -std=gnu++17 accepts -g… yes
checking for g++ -std=gnu++17 option to enable C++11 features… none needed
checking for stdio.h… yes
checking for stdlib.h… yes
checking for string.h… yes
checking for inttypes.h… yes
checking for stdint.h… yes
checking for strings.h… yes
checking for sys/stat.h… yes
checking for sys/types.h… yes
checking for unistd.h… yes
checking for _Bool… no
checking for stdbool.h that conforms to C99 or later… yes
checking for error_at_line… yes
checking for gcc… gcc
checking whether the compiler supports GNU C… yes
checking whether gcc accepts -g… yes
checking for gcc option to enable C11 features… none needed
checking for brew… no
checking for XML_ParserCreate in -lexpat… yes
checking for udunits2.h… yes
checking for ut_read_xml in -ludunits2… yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 13.3.0’
g++ -std=gnu++17 -I"/opt/ebsofts/R/4.4.2-gfbf-2024a/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -I’/home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include’ -I/opt/ebsofts/FriBidi/1.0.15-GCCcore-13.3.0/include -I/opt/ebsofts/HarfBuzz/9.0.0-GCCcore-13.3.0/include -I/opt/ebsofts/Tk/8.6.14-GCCcore-13.3.0/include -I/opt/ebsofts/cURL/8.7.1-GCCcore-13.3.0/include -I/opt/ebsofts/OpenSSL/3/include -I/opt/ebsofts/libgit2/1.8.1-GCCcore-13.3.0/include -I/opt/ebsofts/Java/17.0.2/include -I/opt/ebsofts/LibTIFF/4.6.0-GCCcore-13.3.0/include -I/opt/ebsofts/libjpeg-turbo/3.0.1-GCCcore-13.3.0/include -I/opt/ebsofts/libpng/1.6.43-GCCcore-13.3.0/include -I/opt/ebsofts/PCRE2/10.43-GCCcore-13.3.0/include -I/opt/ebsofts/SQLite/3.45.3-GCCcore-13.3.0/include -I/opt/ebsofts/zlib/1.3.1-GCCcore-13.3.0/include -I/opt/ebsofts/XZ/5.4.5-GCCcore-13.3.0/include -I/opt/ebsofts/bzip2/1.0.8-GCCcore-13.3.0/include -I/opt/ebsofts/ncurses/6.5-GCCcore-13.3.0/include -I/opt/ebsofts/libreadline/8.2-GCCcore-13.3.0/include -I/opt/ebsofts/cairo/1.18.0-GCCcore-13.3.0/include -I/opt/ebsofts/libGLU/9.0.3-GCCcore-13.3.0/include -I/opt/ebsofts/Mesa/24.1.3-GCCcore-13.3.0/include -I/opt/ebsofts/X11/20240607-GCCcore-13.3.0/include -I/opt/ebsofts/pkgconf/2.2.0-GCCcore-13.3.0/include -I/opt/ebsofts/FFTW/3.3.10-GCC-13.3.0/include -I/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/include -I/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/include/flexiblas -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/ebsofts/R/4.4.2-gfbf-2024a/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -I’/home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include’ -I/opt/ebsofts/FriBidi/1.0.15-GCCcore-13.3.0/include -I/opt/ebsofts/HarfBuzz/9.0.0-GCCcore-13.3.0/include -I/opt/ebsofts/Tk/8.6.14-GCCcore-13.3.0/include -I/opt/ebsofts/cURL/8.7.1-GCCcore-13.3.0/include -I/opt/ebsofts/OpenSSL/3/include -I/opt/ebsofts/libgit2/1.8.1-GCCcore-13.3.0/include -I/opt/ebsofts/Java/17.0.2/include -I/opt/ebsofts/LibTIFF/4.6.0-GCCcore-13.3.0/include -I/opt/ebsofts/libjpeg-turbo/3.0.1-GCCcore-13.3.0/include -I/opt/ebsofts/libpng/1.6.43-GCCcore-13.3.0/include -I/opt/ebsofts/PCRE2/10.43-GCCcore-13.3.0/include -I/opt/ebsofts/SQLite/3.45.3-GCCcore-13.3.0/include -I/opt/ebsofts/zlib/1.3.1-GCCcore-13.3.0/include -I/opt/ebsofts/XZ/5.4.5-GCCcore-13.3.0/include -I/opt/ebsofts/bzip2/1.0.8-GCCcore-13.3.0/include -I/opt/ebsofts/ncurses/6.5-GCCcore-13.3.0/include -I/opt/ebsofts/libreadline/8.2-GCCcore-13.3.0/include -I/opt/ebsofts/cairo/1.18.0-GCCcore-13.3.0/include -I/opt/ebsofts/libGLU/9.0.3-GCCcore-13.3.0/include -I/opt/ebsofts/Mesa/24.1.3-GCCcore-13.3.0/include -I/opt/ebsofts/X11/20240607-GCCcore-13.3.0/include -I/opt/ebsofts/pkgconf/2.2.0-GCCcore-13.3.0/include -I/opt/ebsofts/FFTW/3.3.10-GCC-13.3.0/include -I/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/include -I/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/include/flexiblas -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c tokenizer.cpp -o tokenizer.o
g++ -std=gnu++17 -I"/opt/ebsofts/R/4.4.2-gfbf-2024a/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=0 -I’/home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include’ -I/opt/ebsofts/FriBidi/1.0.15-GCCcore-13.3.0/include -I/opt/ebsofts/HarfBuzz/9.0.0-GCCcore-13.3.0/include -I/opt/ebsofts/Tk/8.6.14-GCCcore-13.3.0/include -I/opt/ebsofts/cURL/8.7.1-GCCcore-13.3.0/include -I/opt/ebsofts/OpenSSL/3/include -I/opt/ebsofts/libgit2/1.8.1-GCCcore-13.3.0/include -I/opt/ebsofts/Java/17.0.2/include -I/opt/ebsofts/LibTIFF/4.6.0-GCCcore-13.3.0/include -I/opt/ebsofts/libjpeg-turbo/3.0.1-GCCcore-13.3.0/include -I/opt/ebsofts/libpng/1.6.43-GCCcore-13.3.0/include -I/opt/ebsofts/PCRE2/10.43-GCCcore-13.3.0/include -I/opt/ebsofts/SQLite/3.45.3-GCCcore-13.3.0/include -I/opt/ebsofts/zlib/1.3.1-GCCcore-13.3.0/include -I/opt/ebsofts/XZ/5.4.5-GCCcore-13.3.0/include -I/opt/ebsofts/bzip2/1.0.8-GCCcore-13.3.0/include -I/opt/ebsofts/ncurses/6.5-GCCcore-13.3.0/include -I/opt/ebsofts/libreadline/8.2-GCCcore-13.3.0/include -I/opt/ebsofts/cairo/1.18.0-GCCcore-13.3.0/include -I/opt/ebsofts/libGLU/9.0.3-GCCcore-13.3.0/include -I/opt/ebsofts/Mesa/24.1.3-GCCcore-13.3.0/include -I/opt/ebsofts/X11/20240607-GCCcore-13.3.0/include -I/opt/ebsofts/pkgconf/2.2.0-GCCcore-13.3.0/include -I/opt/ebsofts/FFTW/3.3.10-GCC-13.3.0/include -I/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/include -I/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/include/flexiblas -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c udunits.cpp -o udunits.o
g++ -std=gnu++17 -shared -L/opt/ebsofts/R/4.4.2-gfbf-2024a/lib64/R/lib -L/opt/ebsofts/FriBidi/1.0.15-GCCcore-13.3.0/lib64 -L/opt/ebsofts/FriBidi/1.0.15-GCCcore-13.3.0/lib -L/opt/ebsofts/HarfBuzz/9.0.0-GCCcore-13.3.0/lib64 -L/opt/ebsofts/HarfBuzz/9.0.0-GCCcore-13.3.0/lib -L/opt/ebsofts/Tk/8.6.14-GCCcore-13.3.0/lib64 -L/opt/ebsofts/Tk/8.6.14-GCCcore-13.3.0/lib -L/opt/ebsofts/cURL/8.7.1-GCCcore-13.3.0/lib64 -L/opt/ebsofts/cURL/8.7.1-GCCcore-13.3.0/lib -L/opt/ebsofts/OpenSSL/3/lib64 -L/opt/ebsofts/OpenSSL/3/lib -L/opt/ebsofts/libgit2/1.8.1-GCCcore-13.3.0/lib64 -L/opt/ebsofts/libgit2/1.8.1-GCCcore-13.3.0/lib -L/opt/ebsofts/Java/17.0.2/lib64 -L/opt/ebsofts/Java/17.0.2/lib -L/opt/ebsofts/LibTIFF/4.6.0-GCCcore-13.3.0/lib64 -L/opt/ebsofts/LibTIFF/4.6.0-GCCcore-13.3.0/lib -L/opt/ebsofts/libjpeg-turbo/3.0.1-GCCcore-13.3.0/lib64 -L/opt/ebsofts/libjpeg-turbo/3.0.1-GCCcore-13.3.0/lib -L/opt/ebsofts/libpng/1.6.43-GCCcore-13.3.0/lib64 -L/opt/ebsofts/libpng/1.6.43-GCCcore-13.3.0/lib -L/opt/ebsofts/PCRE2/10.43-GCCcore-13.3.0/lib64 -L/opt/ebsofts/PCRE2/10.43-GCCcore-13.3.0/lib -L/opt/ebsofts/SQLite/3.45.3-GCCcore-13.3.0/lib64 -L/opt/ebsofts/SQLite/3.45.3-GCCcore-13.3.0/lib -L/opt/ebsofts/zlib/1.3.1-GCCcore-13.3.0/lib64 -L/opt/ebsofts/zlib/1.3.1-GCCcore-13.3.0/lib -L/opt/ebsofts/XZ/5.4.5-GCCcore-13.3.0/lib64 -L/opt/ebsofts/XZ/5.4.5-GCCcore-13.3.0/lib -L/opt/ebsofts/bzip2/1.0.8-GCCcore-13.3.0/lib64 -L/opt/ebsofts/bzip2/1.0.8-GCCcore-13.3.0/lib -L/opt/ebsofts/ncurses/6.5-GCCcore-13.3.0/lib64 -L/opt/ebsofts/ncurses/6.5-GCCcore-13.3.0/lib -L/opt/ebsofts/libreadline/8.2-GCCcore-13.3.0/lib64 -L/opt/ebsofts/libreadline/8.2-GCCcore-13.3.0/lib -L/opt/ebsofts/cairo/1.18.0-GCCcore-13.3.0/lib64 -L/opt/ebsofts/cairo/1.18.0-GCCcore-13.3.0/lib -L/opt/ebsofts/libGLU/9.0.3-GCCcore-13.3.0/lib64 -L/opt/ebsofts/libGLU/9.0.3-GCCcore-13.3.0/lib -L/opt/ebsofts/Mesa/24.1.3-GCCcore-13.3.0/lib64 -L/opt/ebsofts/Mesa/24.1.3-GCCcore-13.3.0/lib -L/opt/ebsofts/X11/20240607-GCCcore-13.3.0/lib64 -L/opt/ebsofts/X11/20240607-GCCcore-13.3.0/lib -L/opt/ebsofts/pkgconf/2.2.0-GCCcore-13.3.0/lib64 -L/opt/ebsofts/pkgconf/2.2.0-GCCcore-13.3.0/lib -L/opt/ebsofts/FFTW/3.3.10-GCC-13.3.0/lib64 -L/opt/ebsofts/FFTW/3.3.10-GCC-13.3.0/lib -L/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/lib64 -L/opt/ebsofts/FlexiBLAS/3.4.4-GCC-13.3.0/lib -L/opt/ebsofts/GCCcore/13.3.0/lib64 -L/opt/ebsofts/GCCcore/13.3.0/lib -o units.so RcppExports.o tokenizer.o udunits.o -lexpat -lexpat -ludunits2 -L/opt/ebsofts/R/4.4.2-gfbf-2024a/lib64/R/lib -lR
installing to /home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-units/00new/units/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

*** caught illegal operation ***
address 0x15004256bc0d, cause ‘illegal operand’

Traceback:
1: ud_init(path)
2: load_units_xml()
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(“units”, “/home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-units/00new”)
An irrecoverable exception occurred. R is aborting now …
ERROR: loading failed

removing ‘/home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/units’
ERROR: dependency ‘units’ is not available for package ‘sf’

removing ‘/home/users/c/cottierf/R/x86_64-pc-linux-gnu-library/4.4/sf’

The downloaded source packages are in
‘/tmp/RtmpmgD2OA/downloaded_packages’
Warning messages:
1: In install.packages(“sf”) :
installation of package ‘units’ had non-zero exit status
2: In install.packages(“sf”) :
installation of package ‘sf’ had non-zero exit status

Some additional informations:

R> sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 9.6 (Blue Onyx)

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS; LAPACK version 3.12.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Zurich
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Rcpp_1.1.0

loaded via a namespace (and not attached):
[1] compiler_4.4.2 tools_4.4.2

Adrien.Albert · November 13, 2025, 10:46am

hi @Fabien.Cottier

Indeed I get an error with installing units. However I needed to load CMake in addition of R, to compile depedencies:

ml GCC/13.3.0 R CMake

Here my install R script, but the units-1.0-1 seems incompatible or (missing something I do not know) installing the previous version works:

$ cat install_R_pkg.R

installed.packages()
install.packages("sf", type = "source")
install.packages("https://cran.r-project.org/src/contrib/Archive/units/units_0.8-7.tar.gz", repos = NULL, type = "source", lib="~/Rpackages")


find.package("units", verbose = TRUE)
packageVersion("units")

(baobab)-[alberta@cpu349 R]$ Rscript install_R_pkg.R
[... Build blabla...]

installing to /home/users/a/alberta/Rpackages/00LOCK-units/00new/units/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (units)
[1] "/home/users/a/alberta/Rpackages/units"
[1] ‘0.8.7’

TADA !

Fabien.Cottier · November 14, 2025, 1:28pm

Ciao Adrien,

Merci bien de ton message.J’ai effectivement pu réussir à installer le package “units”, selon tes indications (à la fois la version 0.8-7 et 1.0.0). Il semble que l’erreur soit associée avec le module UDUNITS/2.2.28. Si le module n’est pas “load”, alors “units” est installé correctement.

Je rencontre par contre toujours une erreur avec l’installation du package “sf” à proprement parlé, il semble que le programme ne puisse pas detecté les libraries GDAL, même si le module est chargé (l’erreur semble similaire à celle raportée ici: Problem install 'sf' package in R/4.2.1 )

Encore merci pour ton assistance,


module load foss/2024a  GEOS/3.12.2 GDAL/3.10.0 PROJ/9.4.1  CMake R/4.4.2

R

install.packages(“sf”)

Erreur

installing source package ‘sf’ …
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config… /opt/ebsofts/GDAL/3.10.0-foss-2024a/bin/gdal-config
checking gdal-config usability… yes
configure: GDAL: 3.10.0
checking GDAL version >= 2.0.1… yes
checking for gcc… gcc
checking whether the C compiler works… yes
checking for C compiler default output file name… a.out
checking for suffix of executables…
checking whether we are cross compiling… no
checking for suffix of object files… o
checking whether the compiler supports GNU C… yes
checking whether gcc accepts -g… yes
checking for gcc option to enable C11 features… none needed
checking for stdio.h… yes
checking for stdlib.h… yes
checking for string.h… yes
checking for inttypes.h… yes
checking for stdint.h… yes
checking for strings.h… yes
checking for sys/stat.h… yes
checking for sys/types.h… yes
checking for unistd.h… yes
checking for gdal.h… yes
checking GDAL: linking with --libs only… no
checking GDAL: linking with --libs and --dep-libs… no
/opt/ebsofts/binutils/2.42-GCCcore-13.3.0/bin/ld: warning: libOpenCL.so.1, needed by /opt/ebsofts/GDAL/3.10.0-foss-2024a/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/opt/ebsofts/binutils/2.42-GCCcore-13.3.0/bin/ld: /opt/ebsofts/GDAL/3.10.0-foss-2024a/lib/libgdal.so: undefined reference to clReleaseMemObject@OPENCL_1.0' /opt/ebsofts/binutils/2.42-GCCcore-13.3.0/bin/ld: /opt/ebsofts/GDAL/3.10.0-foss-2024a/lib/libgdal.so: undefined reference to clGetKernelWorkGroupInfo@OPENCL_1.0’

[more similar messages]

collect2: error: ld returned 1 exit status
/opt/ebsofts/binutils/2.42-GCCcore-13.3.0/bin/ld: cannot find -lOpenCL: No such file or directory
collect2: error: ld returned 1 exit status
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
*** Installing this package from source requires the prior

Fabien.Cottier · November 14, 2025, 3:55pm

Here are some supplementary information. The error is caused by GDAL 3.10 missing some critical libraries. In addition, GCC 13.3.0 does not have the library libOpenCL.so

Indeed, running the following command throws an error

gdalinfo --version

Caught signal 4 (Illegal instruction: illegal operand)
==== backtrace (tid:2407155) ====
0 0x000000000003ebf0 __GI___sigaction() :0
1 0x00000000001954cd osgeo::proj::util::LocalName::LocalName() :0
2 0x0000000000195568 osgeo::proj::util::NameSpace::createGLOBAL() :0
3 0x00000000000d6df7 __static_initialization_and_destruction_0() static.cpp:0
4 0x000000000000551e call_init() /usr/src/debug/glibc-2.34-168.el9_6.23.x86_64/elf/dl-init.c:70
5 0x000000000000560c _dl_init() /usr/src/debug/glibc-2.34-168.el9_6.23.x86_64/elf/dl-init.c:117
6 0x000000000001da9a _dl_start_user() :0

On the other hand, I am able to install sf if I load GCC/13.2.0 OpenMPI/4.1.6 and GDAL/3.10.0 instead and then Rv4.4.1 (instead of R4.4.2).

Running gdalinfo --versionwith GDAL 3.9,00 give the following output ": GDAL 3.9.0, released 2024/05/07

I am not sure what is going wrong, but it seems that GCC 13.3.0 and GDAL 3.10 may be corrupted.

Yann.Sagon · November 17, 2025, 1:33pm

Dear @Fabien.Cottier

I found something interesting. We are building Baobab software on an apptainer container. And it appears that when we start apptainer with gpu support, the needed libs are automagically available and gdal used them. Later when you run the soft, the library isn’t available anymore.

I’ll rebuild gdal, but I need first to check how to ignore the library OpenCL.

Fabien.Cottier · November 17, 2025, 2:00pm

HI Yann,

That’s interesting. I am not enough well versed in Linux sytems to be of much assistance, here. However, while I was trying to find a solution on Friday, chatGPT suggested that I looked for locations where the library libOpenCL.so was installed.

I did not find any within the GCC libraries using the linux shell “find” tool, but openCL was installed on multiple CUDA libraries, e.g. /opt/ebsofts/CUDA/12.4.0/targets/x86_64-linux/lib/libOpenCL.so.

Not sure if this helps.

Yann.Sagon · November 18, 2025, 10:32am

Dear @Fabien.Cottier

I’ve recompiled GDAL, GEOS and PROJ. It should work better now, please give a try.

Best regards

Yann

Fabien.Cottier · November 19, 2025, 8:22am

Hi @yann.Sagon,

Thanks. I can confirm that everything is now working. I was able to recompile the sf and other related packages under R 4.4.2 without any issue. It seemst to be working well, as I can judge.
Just of out of curiosity: how did you solve the issue?

Fabien

Yann.Sagon · November 19, 2025, 9:12am

I’ve recompiled the software on a “legacy” compute node without gpu, thus libOpenCL.so not present and not linked.