Cannot install R packages on top of EESSI R #1456
Description
I am trying to install the lme4 R package on top of the R/4.5.1-gfbf-2025a module in EESSI 2025.06 (for which no R-bundle-Bioconductor or R-bundle-CRAN modules are available yet). The commands I came up with based on https://www.eessi.io/docs/using_eessi/building_on_eessi/#manually-building-software-on-top-of-eessi-without-easybuild are:
# Load EESSI environment
module --force purge
unset MODULEPATH
module use /cvmfs/software.eessi.io/init/modules
module load EESSI/2025.06
module load R/4.5.1-gfbf-2025a
module load buildenv/default-foss-2025a
# Create personal R library dir, adapt this if you do not have VSC variables set...
mkdir -p ${VSC_DATA}/Rlibs/EESSI/${VSC_ARCH_LOCAL}/R-${EBVERSIONR}
grep -qF 'R_LIBS_USER' $VSC_HOME/.Renviron 2>/dev/null || \
echo 'R_LIBS_USER=${VSC_DATA}/Rlibs/EESSI/${VSC_ARCH_LOCAL}/R-${EBVERSIONR}' >> $VSC_HOME/.Renviron
# Install package with explicit mirror
CURL_CA_BUNDLE="/etc/ssl/certs/ca-bundle.crt" Rscript -e \
'install.packages("rbibutils", repos="https://cloud.r-project.org")'
This fails with:
========================================================================
Module for EESSI/2025.06 loaded successfully
Installing package into ‘/vsc-hard-mounts/leuven-data/337/vsc33716/Rlibs/EESSI/icelake/R-4.5.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rbibutils_2.4.1.tar.gz'
Content type 'application/x-gzip' length 1191704 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/share/lmod/lmod/init/bash: line 30: [: too many arguments
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/share/lmod/lmod/init/bash: line 30: [: too many arguments
* installing *source* package ‘rbibutils’ ...
** this is package ‘rbibutils’ version ‘2.4.1’
** package ‘rbibutils’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/share/lmod/lmod/init/bash: line 30: [: too many arguments
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/share/lmod/lmod/init/bash: line 30: [: too many arguments
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/share/lmod/lmod/init/bash: line 30: [: too many arguments
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
Warning in system(paste(cc, "--version"), intern = TRUE) :
running command 'gcc -std=gnu23 --version' had status 1
using C compiler: ‘NA’
gcc -std=gnu23 -I"/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/intel/icelake/software/R/4.5.1-gfbf-2025a/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -O2 -ftree-vectorize -march=native -fno-math-errno -c adsout.c -o adsout.o
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/share/lmod/lmod/init/bash: line 30: [: too many arguments
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
/usr/bin/coreutils: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/lib/../lib64/libm.so.6)
make: *** [/cvmfs/software.eessi.io/versions/2025.06/software/linux/x86_64/intel/icelake/software/R/4.5.1-gfbf-2025a/lib64/R/etc/Makeconf:202: adsout.o] Error 1
ERROR: compilation failed for package ‘rbibutils’
* removing ‘/vsc-hard-mounts/leuven-data/337/vsc33716/Rlibs/EESSI/icelake/R-4.5.1/rbibutils’
The downloaded source packages are in
‘/tmp/RtmpwyuiDm/downloaded_packages’
Warning message:
In install.packages("rbibutils", repos = "https://cloud.r-project.org") :
installation of package ‘rbibutils’ had non-zero exit status
It looks like I can't manage to isolate EESSI from some host executables/libraries like /usr/bin/coreutils and /lib64/libc.so.6.
Are there any suggestions on how to tackle this issue?