These instructions describe how to use the R package move2 on the HPC cluster:

• Interactive sessions
• Slurm batch jobs

On this system, credentials are stored per R session using the keyring env backend (expected behaviour on headless nodes).

~$ srun -p ceab --pty bash

~$ module load R-bundle-CRAN

Start R,

~$ R

Check whether move2 is installed:

> library(move2)

If not installed (typical on HPCs), install it in your user library:

> install.packages("move2", repos = "https://cloud.r-project.org")

The package will be installed under ~/R/x86_64-pc-linux-gnu-library/.

> library(move2)

> movebank_store_credentials(<movebank_user_name>)

You will be prompted once for your Movebank password. Credentials remain valid only for the current R session.

A warning about the env backend may appear. This is expected on this system.

List all accessible studies:

> movebank_download_study_info()

List only studies with download access:

> movebank_download_study_info(i_have_download_access = TRUE)

Query a specific study by ID:

> movebank_download_study_info(id = 2911040)

To avoid repeated warnings about the keyring backend:

suppressWarnings(
  movebank_download_study_info()
)

This does not affect functionality.

Resolve the study ID if you just know the name:

suppressWarnings(
  study_id <- movebank_get_study_id(
    study_id = "Galapagos Albatrosses"
  )
)

Then download data with filters:

suppressWarnings(
  data <- movebank_download_study(
    study_id,
    sensor_type_id = "gps",
    timestamp_start = as.POSIXct("2008-08-01 00:00:00"),
    timestamp_end   = as.POSIXct("2008-08-02 00:00:00")
  )
)

data is returned as a move2 object and can be processed directly with the package’s tools.

• Credentials are session-local (lost on R session exit)
• No persistent encrypted keyring is available on this system
• Warning messages about the env backend are normal
• Authentication happens automatically when calling download functions

Because the system is headless, Movebank credentials must be provided via environment variables (lost on shell session exit).

NEVER hard-code passwords in your R scripts !!

Before submitting the job, export your credentials in the shell.

export MOVEBANK_USER="your_movebank_user_name"
export MOVEBANK_PASSWORD="your_movebank_user_password"

These variables are inherited by the Slurm job.

Example: myRscript.R

library(move2)

# Get credentials from the env vars and store credentials for this Movebank session
movebank_store_credentials(
  Sys.getenv("MOVEBANK_USER"),
  Sys.getenv("MOVEBANK_PASSWORD")
)
# Check available studies
studies <- suppressWarnings(
  movebank_download_study_info(i_have_download_access = TRUE)
)
# show result
print(studies)

Example: run_myRscript.sbatch

#!/bin/bash
#SBATCH --job-name=movebank
#SBATCH --time=01:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1
#SBATCH --output=myRscript_%j.out
#SBATCH --error=myRscript_%j.err

# load R modules
module load R-bundle-CRAN

# launch R script
Rscript myRscript.R

srun_-p ceab run_myRscript.sbatch

• Credentials are lost on shell session exit
• The keyring env backend warning is expected
• Use suppressWarnings() to keep logs clean
• No explicit authentication function necessary
• Do not use interactive prompts in batch jobs