Package: abba 0.2.0

Mike Stackhouse

abba: Batch Execution of R Programs on 'Kubernetes', 'SLURM', and 'Posit Workbench'

Submit and monitor batch execution of R programs across distributed computing backends including 'Kubernetes', 'SLURM', and 'Posit Workbench'. Provides end-user job submission functions, cluster interface functions using 'kubectl' and 'SLURM' commands, and a 'plumber' API template for secure identity segregation. Supports parallel and sequential batch execution, file-based caching to skip unchanged programs, and 'logrx' integration for execution logging.

Authors:Eli Miller [aut], Mike Stackhouse [aut, cre], Ross Didenko [aut], Yevhenii Boiko [aut], Atorus Research, Inc. [cph]

abba_0.2.0.tar.gz
abba_0.2.0.zip(r-4.7)abba_0.2.0.zip(r-4.6)abba_0.2.0.zip(r-4.5)
abba_0.2.0.tgz(r-4.6-any)abba_0.2.0.tgz(r-4.5-any)
abba_0.2.0.tar.gz(r-4.7-any)abba_0.2.0.tar.gz(r-4.6-any)
abba_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
abba/json (API)
NEWS

# Install 'abba' in R:
install.packages('abba', repos = c('https://atorus-research.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/atorus-research/abba/issues

Pkgdown/docs site:https://atorus-research.github.io

On CRAN:

Conda:

5.15 score 2 stars 518 downloads 33 exports 30 dependencies

Last updated from:91a090be04. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE138
source / vignettesOK184
linux-release-x86_64NOTE135
macos-release-arm64NOTE93
macos-oldrel-arm64NOTE84
windows-develNOTE93
windows-releaseNOTE83
windows-oldrelNOTE85
wasm-releaseOK113

Exports:%>%abba_get_batch_logabba_get_batch_statusabba_get_job_logabba_get_job_statusabba_get_k8s_batch_log_localabba_get_k8s_batch_status_localabba_get_k8s_job_log_localabba_get_k8s_job_status_localabba_rslauncher_get_job_status_localabba_rslauncher_get_job_succeeded_localabba_rslauncher_submit_job_localabba_rslauncher_submit_logrx_job_localabba_rslauncher_watch_job_localabba_slurm_get_job_logabba_slurm_get_job_statusabba_slurm_get_job_succeededabba_slurm_submit_jobabba_slurm_watch_jobabba_submit_and_get_logabba_submit_batchabba_submit_batch_and_get_resultsabba_submit_jobabba_submit_k8s_job_and_poll_localabba_submit_k8s_job_localabba_wait_for_batch_logabba_wait_for_job_logabba_watch_k8s_batch_localabba_watch_k8s_job_localcalculate_run_groupcreate_batch_apicreate_batch_jobsubmit_k8s_yaml

Dependencies:askpassclicpp11curldigestdplyrgenericsgluehttr2lifecyclemagrittropensslpillarpkgconfigpurrrR6rappdirsrlangrstudioapistringistringrsystibbletidyrtidyselectutf8uuidvctrswithryaml

abba Options

Rendered fromabba_options.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-14
Started: 2024-03-12

Kubernetes API Setup

Rendered fromk8s_api_setup.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2024-03-12

Kubernetes Batch Jobs

Rendered fromk8s_batch_job.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2024-03-12

Kubernetes Job Submission

Rendered fromk8s_job_submission.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-14
Started: 2024-03-12

SLURM Job Submission

Rendered fromslurm_job_submission.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2024-07-19

Workbench Batch Jobs

Rendered fromworkbench_batch_job.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2024-04-03

Workbench Job Submission

Rendered fromworkbench_job_submission.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-23
Started: 2024-04-03

Readme and manuals

Help Manual

Help pageTopics
Send GET request to get logs of all jobs in a batchabba_get_batch_log
Send GET request to get batch job statusesabba_get_batch_status
Send GET request to get logs of specified Jobsabba_get_job_log
Send GET request to get job statusabba_get_job_status
Return list of logs for jobs that are marked with a given batch IDabba_get_k8s_batch_log_local
Get status of all jobs in a batchabba_get_k8s_batch_status_local
Get log for every job specified in an input vector/listabba_get_k8s_job_log_local
Get status of all pods that belong to a jobabba_get_k8s_job_status_local
Get Workbench job status for a given vector/list of job IDsabba_rslauncher_get_job_status_local
Check whether Workbench jobs have been fully executed.abba_rslauncher_get_job_succeeded_local
Create a job for executing an R programabba_rslauncher_submit_job_local
Execute programs via logrxabba_rslauncher_submit_logrx_job_local
Periodically poll Workbench jobs for status and return their IDs when all job statuses arrive at 'Finished' stateabba_rslauncher_watch_job_local
Return job log for each submitted job IDabba_slurm_get_job_log
Return descriptive job status for slurm jobsabba_slurm_get_job_status
Check whether SLURM jobs have been fully executed.abba_slurm_get_job_succeeded
Submit R program as a SLURM jobabba_slurm_submit_job
Watch SLURM job, periodically polling its execution status.abba_slurm_watch_job
Send job and poll for status. This function sends multiple requests so it won't time out on heavy jobsabba_submit_and_get_log
Submit programs for execution in order defined by structure of input list. Programs inside sublists will be executed in parallel, and sublists themselves would be submitted sequentially.abba_submit_batch
Submit programs for execution in order defined by structure of input list.abba_submit_batch_and_get_results
Send POST request to submit-job endpointabba_submit_job
Submit a job profile for execution on a Kubernetes cluster and poll for completionabba_submit_k8s_job_and_poll_local
Submit an R program for execution on a Kubernetes clusterabba_submit_k8s_job_local
Monitor batch status and retrieve its log when the all jobs in batch finish runningabba_wait_for_batch_log
Monitor job status and retrieve its log when the job finishes runningabba_wait_for_job_log
Watch a K8S batch that has been submitted to Workbench, periodically polling it's execution status.abba_watch_k8s_batch_local
Watch a K8S job that has been submitted to Workbench, periodically polling it's execution status.abba_watch_k8s_job_local
Calculate run_group variable using inputs and outputs of programs supplied by usercalculate_run_group
Create a Batch API or Job file templatecreate_batch_api create_batch_job
Submit a job profile for execution on a Kubernetes clustersubmit_k8s_yaml