R package igraph 2.2.1 failed installation, undefined symbol: glp_at_error

Installation
1

When I try to install igraph 2.2.1 in R on a cluster (CentOS Linux), I receive the following error.

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/u/home/r/rbenitez/R/x86_64-pc-linux-gnu-library-RH7/4.4.0/gcc10.2.0_intel2023.1.0/00LOCK-igraph/00new/igraph/libs/igraph.so’:
/u/home/r/rbenitez/R/x86_64-pc-linux-gnu-library-RH7/4.4.0/gcc10.2.0_intel2023.1.0/00LOCK-igraph/00new/igraph/libs/igraph.so: undefined symbol: glp_at_error
Error: loading failed
Execution halted

I’m trying to perform this installation on R 4.4.0, and here are other modules I have loaded alongside it.

module list
Currently Loaded Modulefiles:

1. IDRE   2) gcc/10.2.0   3) intel/2022.1.1 <aL>   4) java/jdk-11.0.14 <aL>   5) glpk/5.0 <aL>   6) R/4.4.0

Key:
  =auto-loaded

igraph 2.2.1 will successfully install on this system if I load R 4.2.2 for example, where it doesn’t require the auto-loaded modules as prerequisites.

Here is my session info, any help would be greatly appreciated.

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /u/local/compilers/intel/oneapi/2022.1.1/mkl/2022.0.1/lib/intel64/libmkl_gf_lp64.so.2;  LAPACK version 3.9.0

locale:
\[1\] C

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
\[1\] compiler_4.4.0
2

The system finds the GLPK library during compilation, but not when loading the package.

Reasons could be:

  • You have different modules loaded while compiling, or using igraph.
  • Something is just wrong with the way the module system exposes shared libraries.

My suggestions:

  • Try compiling without loading the GLPK module at all.
  • Do not use the Intel compiler and do not load its module.
  • If you post the full terminal transcript, starting with a fresh login to the server, and including module list, we might be able to make further suggestions.
3

Did you manage to sort it out, and if yes, can you share what you did?

4

Unfortunately I am not able to unload the glpk or intel modules. They are considered prerequisites for loading R/4.4.0 in this situation. I suspect the glpk or intel modules may be, in part, the culprit because igraph 2.2.1 will install on R 4.2.2 on this system, where this version of R does not require glpk/5.0 or intel/2022.1.1 as prerequisites. Here is the terminal transcript with the login to the server, as well as information about the modules I’m using.

Last login: Sat Nov 22 01:39:16 2025 from 98.153.226.245
Welcome to the Hoffman2 Cluster!

Hoffman2 Home Page:     http://www.hoffman2.idre.ucla.edu
Consulting:             https://support.idre.ucla.edu/helpdesk

All login nodes should be accessed via "hoffman2.idre.ucla.edu".

Please do NOT compute on the login nodes.

Processes running on the login nodes which seriously degrade others'
use of the system may be terminated without warning.  Use qrsh to obtain
an interactive shell on a compute node for CPU or I/O intensive tasks.

The following news items are currently posted:

   NoMachine Remote Desktop Nodes Updated to version 9.1.24
   How to change the time request on pending jobs
   Stata Upgraded to version 19.5
   Visual Studio Code Version Supported by the Hoffman2 Cluster
   SIM the new account management application is now live
   Anaconda initialization and virtual desktop
   How to modify any resource requested in a pending job
   x2go select MATE or XFCE desktop environment instead of GNOME
   GPU nodes available
   IDRE Workshops and Training Sessions

Enter shownews to read the full text of a news item.
[rbenitez@login1 ~]$ module load gcc/10.2.0; module load R/4.4.0
Loading R/4.4.0
  Loading requirement: intel/2022.1.1 java/jdk-11.0.14 glpk/5.0

[rbenitez@login4 ~]$ module list
Currently Loaded Modulefiles:
 1) IDRE   2) intel/2020.4(default)   3) gcc/10.2.0   4) intel/2022.1.1 <aL>   5) java/jdk-11.0.14 <aL>   6) glpk/5.0 <aL>   7) R/4.4.0

Key:
(symbolic-version)  <module-tag>  <aL>=auto-loaded

[rbenitez@login4 ~]$ module unload glpk/5.0
Unloading glpk/5.0
  ERROR: glpk/5.0 cannot be unloaded due to a prereq.
    HINT: Might try "module unload R/4.4.0" first.

[rbenitez@login4 ~]$ module unload intel/2022.1.1
Unloading intel/2022.1.1
  ERROR: intel/2022.1.1 cannot be unloaded due to a prereq.
    HINT: Might try "module unload R/4.4.0" first.