Package: rworkflows 1.0.3

Brian Schilder

rworkflows: Test, Document, Containerise, and Deploy R Packages

Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers. rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action.

Authors:Brian Schilder [aut, cre], Alan Murphy [aut, ctb], Nathan Skene [aut]

rworkflows_1.0.3.tar.gz
rworkflows_1.0.3.zip(r-4.5)rworkflows_1.0.3.zip(r-4.4)rworkflows_1.0.3.zip(r-4.3)
rworkflows_1.0.3.tgz(r-4.4-any)rworkflows_1.0.3.tgz(r-4.3-any)
rworkflows_1.0.3.tar.gz(r-4.5-noble)rworkflows_1.0.3.tar.gz(r-4.4-noble)
rworkflows_1.0.3.tgz(r-4.4-emscripten)rworkflows_1.0.3.tgz(r-4.3-emscripten)
rworkflows.pdf |rworkflows.html✨
rworkflows/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/neurogenomics/rworkflows/issues

Datasets:

On CRAN:

softwareworkflowmanagementbioconductorcontainerscontinuous-integrationdockerdockerhubgithub-actionsreproducibilityworkflows

7.65 score 75 stars 6 scripts 333 downloads 22 exports 60 dependencies

Last updated 2 months agofrom:1908435f99. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winERRORNov 01 2024
R-4.5-linuxERRORNov 01 2024
R-4.4-winERRORNov 01 2024
R-4.4-macERRORNov 01 2024
R-4.3-winERRORNov 01 2024
R-4.3-macERRORNov 01 2024

Exports:bioc_r_versionsconda_exportconstruct_authorsconstruct_conda_ymlconstruct_contconstruct_runnersdt_to_descfill_descriptionget_descriptionget_hexinfer_biocviewsinfer_depsinfer_docker_orgis_ghause_badgesuse_codespaceuse_dockerfileuse_issue_templateuse_readmeuse_vignette_dockeruse_vignette_getstarteduse_workflow

Dependencies:askpassbadgerBiocManagerclicliprcolorspacecrayoncredentialscurldata.tabledescdigestdlstatsfansifarverfsgertggplot2ghgitcredsgluegtableherehttr2iniisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmeopensslpillarpkgconfigpurrrR6rappdirsRColorBrewerrenvrlangrprojrootrstudioapirvcheckscalessystibbleusethisutf8vctrsviridisLitewhiskerwithryamlyulab.utilszip

Bioconductor

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered frombioconductor.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-12-29
Started: 2023-09-14

Dependency graph

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered fromdepgraph.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-12-29
Started: 2022-12-09

Docker/Singularity Containers

Authors: `r auths <- eval(parse(text = gsub("person","c",read.dcf("../DESCRIPTION", fields = "Authors@R"))));paste(auths[names(auths)=="given"],auths[names(auths)=="family"], collapse = ", ")`

Rendered fromdocker.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-12-29
Started: 2022-11-06

Repositories report

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered fromrepos.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-12-29
Started: 2022-12-14

Get Started

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered fromrworkflows.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-12-29
Started: 2022-11-07

Readme and manuals

Help Manual

Help pageTopics
Bioconductor / R versionsbioc_r_versions
Static Bioc packages listbiocpkgtools_db
Conda exportconda_export
Construct authorsconstruct_authors
Construct a conda yamlconstruct_conda_yml
Construct containers listconstruct_cont
Construct runnersconstruct_runners
data.table to descdt_to_desc
Fill _DESCRIPTION_fill_description
Get DESCRIPTIONget_description
Get hexget_hex
Infer biocViewsinfer_biocviews
Infer dependenciesinfer_deps
Infer Docker registry organisation nameinfer_docker_org
Is GitHub Actionis_gha
Use badgesuse_badges
Use Codespaceuse_codespace
Use Dockerfileuse_dockerfile
Use Issue Templateuse_issue_template
Use READMEuse_readme
Use vignette: Dockeruse_vignette_docker
Use vignette: Get starteduse_vignette_getstarted
Use GitHub Actions workflowuse_workflow