Dear HPC team and colleagues,
I’ve been trying to install the package “sf” in R/4.2.1 for the past day but keep getting an error message. All the other packages have been updated to ensure that it’s not coming from that. I’ve successfully installed other packages so my environment is apparently set up correctly.
“sf” requires GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3 (CRAN - Package sf).
So I’m loading the following modules:
module load foss/2022a GDAL/3.5.0 GEOS/3.10.3 PROJ/9.0.0 R/4.2.1
When installing the “sf” package, the error is the following :
[…]
checking for gdal.h… yes
checking GDAL: linking with --libs only… no
checking GDAL: linking with --libs and --dep-libs… no
/opt/ebsofts/binutils/2.38-GCCcore-11.3.0/bin/ld: /opt/ebsofts/GDAL/3.5.0-foss-2022a/lib/libgdal.so: undefined reference tologf@GLIBC_2.27' collect2: error: ld returned 1 exit status /opt/ebsofts/binutils/2.38-GCCcore-11.3.0/bin/ld: /opt/ebsofts/GDAL/3.5.0-foss-2022a/lib/libgdal.so: undefined reference to
logf@GLIBC_2.27’
collect2: error: ld returned 1 exit status
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ‘sf’
- removing ‘/home/users/r/richetta/Rpackages/sf’
Could someone please help me understand where the issue is coming from ?
All the best, Cécile.