slurmR 0.5-4

slurmR 0.5-3

Fixed bug in command line tool slurmr that overwrites source file when located in the same folder.

New integer method for get_tmp_path, get_job_name, and get_job_id. This is a fix for issue #29 (first reported by @thistleknot.)

sourceSlurm(plan = "collect") won’t wait forever.
More verbose error messages when Slurm_collect returns with errors.
The function sacct() now doesn’t fail when accounting is not available.
slurmR now has a Dockerimage that can be used to test with a Slurm cluster. The docker image can be started from within R (if Docker is available).
makeSlurmCluster()s default tmp_path is now opts_slurmR$get_tmp_path().
New functions slurmr_docker_* provide a wrapper to interact with the Dockerimage of slurmR.

Minor release.

Added a preamble option for Slurm batch scripts. This allows the user to specify commands that need to be added to the script, e.g., module load.
preamble can be specified via opts_slurmR$set_preamble() or directly when calling Slurm_*apply.
Added the function opts_slurmR$reset().

sourceSlurm() was using a file created at tempdir() which was deleted, and thus, unavailable to be used by sbatch. Tempfiles like those are now created at dirname(tempdir()).

Minor release.

Fixed bug when collecting failed jobs. slurmR would fail to correctly list failed jobs and thus to collect outputs. This would also would affect when trying to collect partially resubmitted jobs.
Slurm options passed via opts_slurmR are now passed to Slurm_*apply as documented. Thanks to Gregory Penn (gregorypenn) who reported the bug.
slurmr_cmd now expands the cmd_path.

Increased code coverage.
The function wait_slurm() is now exported and documented.
Each line in the written R script is now wrapped with a custom tryCatch function (tcq). On error, this new function will collect both the expression called, the error message, and will quit the R session, so now the user has a better description of possible errors, e.g. missing packages.